Starting phenix.real_space_refine
on Tue Mar  3 19:41:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xp4_33364/03_2026/7xp4_33364.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xp4_33364/03_2026/7xp4_33364.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xp4_33364/03_2026/7xp4_33364.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xp4_33364/03_2026/7xp4_33364.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xp4_33364/03_2026/7xp4_33364.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xp4_33364/03_2026/7xp4_33364.cif"
  }
  resolution = 3.01
  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=   0.001 sd=   0.023
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      49      5.16       5
     C    5382      2.51       5
     N    1456      2.21       5
     O    1550      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8437
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1964
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 240, 1964
          Classifications: {'peptide': 240}
          Link IDs: {'PTRANS': 6, 'TRANS': 233}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2616
          Classifications: {'peptide': 341}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 981
          Classifications: {'peptide': 129}
          Link IDs: {'PTRANS': 5, 'TRANS': 123}
    Chain: "R"
      Number of atoms: 2440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2440
          Classifications: {'peptide': 299}
          Link IDs: {'PTRANS': 8, 'TRANS': 290}
  Time building chain proxies: 1.81, per 1000 atoms: 0.21
  Number of scatterers: 8437
  At special positions: 0
  Unit cell: (83.2, 101.92, 134.16, 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      49     16.00
     O    1550      8.00
     N    1456      7.00
     C    5382      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  23 " - pdb=" SG  CYS N  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 100 " - pdb=" SG  CYS N 108 " 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: 0.73
  Conformation dependent library (CDL) restraints added in 311.0 milliseconds
  

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2008

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      45.5% alpha, 19.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 36
    Processing helix  chain 'A' and resid 48 through 60
      removed outlier: 3.562A  pdb=" N   LEU A  59 " --> pdb=" O   GLN A  55 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   HIS A  60 " --> pdb=" O   MET A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 103
    Processing helix  chain 'A' and resid 117 through 133
      removed outlier: 4.072A  pdb=" N   GLN A 122 " --> pdb=" O   TYR A 118 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   GLU A 123 " --> pdb=" O   ASN A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 138
      removed outlier: 3.784A  pdb=" N   ARG A 138 " --> pdb=" O   ARG A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 159
    Processing helix  chain 'A' and resid 162 through 167
      removed outlier: 4.214A  pdb=" N   TYR A 166 " --> pdb=" O   LYS A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 206
    Processing helix  chain 'A' and resid 222 through 247
      removed outlier: 3.967A  pdb=" N   ASN A 226 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 37
      removed outlier: 4.111A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 3.702A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.774A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'N' and resid 63 through 66
    Processing helix  chain 'N' and resid 88 through 92
    Processing helix  chain 'R' and resid 4 through 39
      removed outlier: 4.814A  pdb=" N   SER R  10 " --> pdb=" O   PRO R   6 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 42 through 70
    Processing helix  chain 'R' and resid 77 through 111
      removed outlier: 3.584A  pdb=" N   ILE R  82 " --> pdb=" O   ILE R  78 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   PHE R  94 " --> pdb=" O   VAL R  90 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 115 through 124
      removed outlier: 4.103A  pdb=" N   ARG R 124 " --> pdb=" O   HIS R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 124 through 151
      removed outlier: 3.615A  pdb=" N   VAL R 128 " --> pdb=" O   ARG R 124 " (cutoff:3.500A)
      Proline residue:  R 136  - end of helix
      removed outlier: 3.643A  pdb=" N   PHE R 139 " --> pdb=" O   GLY R 135 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 155 through 160
    Processing helix  chain 'R' and resid 176 through 213
      removed outlier: 4.864A  pdb=" N   VAL R 186 " --> pdb=" O   LEU R 182 " (cutoff:3.500A)
      Proline residue:  R 187  - end of helix
      removed outlier: 3.933A  pdb=" N   HIS R 212 " --> pdb=" O   LYS R 208 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 218 through 250
    Processing helix  chain 'R' and resid 257 through 283
      removed outlier: 3.934A  pdb=" N   PHE R 263 " --> pdb=" O   PRO R 259 " (cutoff:3.500A)
      Proline residue:  R 272  - end of helix
      Proline residue:  R 276  - end of helix
    Processing helix  chain 'R' and resid 283 through 301
    Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 79
      removed outlier: 4.609A  pdb=" N   VAL A  89 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   GLY A  43 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   ARG A  38 " --> pdb=" O   ALA A 108 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   ILE A 110 " --> pdb=" O   ARG A  38 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   LEU A  40 " --> pdb=" O   ILE A 110 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   VAL A 112 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   LEU A  42 " --> pdb=" O   VAL A 112 " (cutoff:3.500A)
      removed outlier: 8.681A  pdb=" N   ASP A 114 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   ILE A 109 " --> pdb=" O   ILE A 143 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   PHE A 145 " --> pdb=" O   ILE A 109 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   PHE A 111 " --> pdb=" O   PHE A 145 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ASN A 147 " --> pdb=" O   PHE A 111 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   VAL A 113 " --> pdb=" O   ASN A 147 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   VAL A 142 " --> pdb=" O   TYR A 215 " (cutoff:3.500A)
      removed outlier: 7.837A  pdb=" N   HIS A 217 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LEU A 144 " --> pdb=" O   HIS A 217 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51
      removed outlier: 5.779A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 3.762A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105
      removed outlier: 6.377A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.506A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.722A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.571A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.981A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.867A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.110A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ASN B 295 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 7
      removed outlier: 3.541A  pdb=" N   GLN N   6 " --> pdb=" O   ALA N  24 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 12 through 13
      removed outlier: 7.160A  pdb=" N   MET N  35 " --> pdb=" O   ASP N  51 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   ASP N  51 " --> pdb=" O   MET N  35 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   TRP N  37 " --> pdb=" O   VAL N  49 " (cutoff:3.500A)

    463 hydrogen bonds defined for protein.
    1338 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: 1.34

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2722
        1.34 -     1.46: 1493
        1.46 -     1.58: 4332
        1.58 -     1.69: 0
        1.69 -     1.81: 70
  Bond restraints: 8617
  Sorted by residual:
  bond pdb=" N   GLY B 341 "
       pdb=" CA  GLY B 341 "
    ideal  model  delta    sigma   weight residual
    1.452  1.494 -0.042 1.05e-02 9.07e+03 1.60e+01
  bond pdb=" N   SER B 342 "
       pdb=" CA  SER B 342 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 1.21e-02 6.83e+03 6.15e+00
  bond pdb=" N   ASN B 340 "
       pdb=" CA  ASN B 340 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.20e-02 6.94e+03 5.36e+00
  bond pdb=" CA  SER B 342 "
       pdb=" CB  SER B 342 "
    ideal  model  delta    sigma   weight residual
    1.531  1.506  0.024 1.52e-02 4.33e+03 2.52e+00
  bond pdb=" CA  GLY B 341 "
       pdb=" C   GLY B 341 "
    ideal  model  delta    sigma   weight residual
    1.519  1.532 -0.013 9.70e-03 1.06e+04 1.86e+00
  ... (remaining 8612 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 11443
        1.75 -     3.49: 185
        3.49 -     5.24: 41
        5.24 -     6.99: 3
        6.99 -     8.73: 1
  Bond angle restraints: 11673
  Sorted by residual:
  angle pdb=" CA  GLY B 341 "
        pdb=" C   GLY B 341 "
        pdb=" O   GLY B 341 "
      ideal   model   delta    sigma   weight residual
     121.41  118.27    3.14 8.80e-01 1.29e+00 1.27e+01
  angle pdb=" C   ASP B 118 "
        pdb=" N   ASN B 119 "
        pdb=" CA  ASN B 119 "
      ideal   model   delta    sigma   weight residual
     121.54  128.23   -6.69 1.91e+00 2.74e-01 1.23e+01
  angle pdb=" C   LYS R 167 "
        pdb=" N   LEU R 168 "
        pdb=" CA  LEU R 168 "
      ideal   model   delta    sigma   weight residual
     122.42  118.04    4.38 1.55e+00 4.16e-01 7.99e+00
  angle pdb=" C   LYS A  98 "
        pdb=" N   TRP A  99 "
        pdb=" CA  TRP A  99 "
      ideal   model   delta    sigma   weight residual
     121.14  116.33    4.81 1.75e+00 3.27e-01 7.57e+00
  angle pdb=" C   GLY A 159 "
        pdb=" N   LYS A 160 "
        pdb=" CA  LYS A 160 "
      ideal   model   delta    sigma   weight residual
     121.54  126.42   -4.88 1.91e+00 2.74e-01 6.52e+00
  ... (remaining 11668 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 4678
       17.58 -    35.15: 369
       35.15 -    52.73: 60
       52.73 -    70.30: 3
       70.30 -    87.88: 4
  Dihedral angle restraints: 5114
    sinusoidal: 2015
      harmonic: 3099
  Sorted by residual:
  dihedral pdb=" CA  CYS N 108 "
           pdb=" C   CYS N 108 "
           pdb=" N   PHE N 109 "
           pdb=" CA  PHE N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.16  -18.84     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  GLY B 185 "
           pdb=" C   GLY B 185 "
           pdb=" N   ASP B 186 "
           pdb=" CA  ASP B 186 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.63   17.37     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CB  CYS N 100 "
           pdb=" SG  CYS N 100 "
           pdb=" SG  CYS N 108 "
           pdb=" CB  CYS N 108 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   66.09   26.91     1      1.00e+01 1.00e-02 1.04e+01
  ... (remaining 5111 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 836
       0.033 -    0.066: 323
       0.066 -    0.099: 105
       0.099 -    0.132: 54
       0.132 -    0.165: 4
  Chirality restraints: 1322
  Sorted by residual:
  chirality pdb=" CB  THR B  47 "
            pdb=" CA  THR B  47 "
            pdb=" OG1 THR B  47 "
            pdb=" CG2 THR B  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.80e-01
  chirality pdb=" CA  TRP A  99 "
            pdb=" N   TRP A  99 "
            pdb=" C   TRP A  99 "
            pdb=" CB  TRP A  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.55e-01
  chirality pdb=" CG  LEU R 168 "
            pdb=" CB  LEU R 168 "
            pdb=" CD1 LEU R 168 "
            pdb=" CD2 LEU R 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 5.02e-01
  ... (remaining 1319 not shown)

  Planarity restraints: 1475
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN G  59 "   -0.061 5.00e-02 4.00e+02   9.21e-02 1.36e+01
        pdb=" N   PRO G  60 "    0.159 5.00e-02 4.00e+02
        pdb=" CA  PRO G  60 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO G  60 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 186 "    0.040 5.00e-02 4.00e+02   6.03e-02 5.81e+00
        pdb=" N   PRO A 187 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A 187 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 187 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP R 218 "   -0.029 5.00e-02 4.00e+02   4.44e-02 3.15e+00
        pdb=" N   PRO R 219 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO R 219 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO R 219 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1472 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 849
        2.74 -     3.28: 8437
        3.28 -     3.82: 14068
        3.82 -     4.36: 15810
        4.36 -     4.90: 28449
  Nonbonded interactions: 67613
  Sorted by model distance:
  nonbonded pdb=" O   VAL N 111 "
            pdb=" OG1 THR N 112 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" OG  SER R 244 "
            pdb=" O   CYS R 264 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OD1 ASN R  31 "
            pdb=" NZ  LYS R 285 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" O   ALA A  44 "
            pdb=" OG  SER A  47 "
     model   vdw
     2.252 3.040
  ... (remaining 67608 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.530
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     8.890
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
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   0.042   8619  Z= 0.167
  Angle     :  0.577   8.735  11677  Z= 0.311
  Chirality :  0.043   0.165   1322
  Planarity :  0.005   0.092   1475
  Dihedral  : 12.473  87.879   3100
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.94 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.26), residues: 1054
  helix:  2.11 (0.24), residues: 437
  sheet:  0.12 (0.34), residues: 227
  loop : -0.91 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B  19 
 TYR   0.011   0.001   TYR B  59 
 PHE   0.023   0.001   PHE R   9 
 TRP   0.025   0.002   TRP R  66 
 HIS   0.003   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8617)
  covalent geometry    : angle       0.57705 (11673)
  SS BOND              : bond        0.00251 (    2)
  SS BOND              : angle       0.80621 (    4)
  hydrogen bonds       : bond        0.16004 (  463)
  hydrogen bonds       : angle       5.96319 ( 1338)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 LYS cc_start: 0.6997 (tptp) cc_final: 0.6764 (tptp)
REVERT: A   23 GLU cc_start: 0.7301 (tp30) cc_final: 0.6910 (tp30)
REVERT: A   29 ASP cc_start: 0.6665 (t0) cc_final: 0.6404 (t0)
REVERT: A   42 LEU cc_start: 0.7911 (mt) cc_final: 0.7696 (mt)
REVERT: A   74 GLU cc_start: 0.7137 (pt0) cc_final: 0.6769 (pt0)
REVERT: A  103 PHE cc_start: 0.7741 (m-10) cc_final: 0.7518 (m-80)
REVERT: A  117 ASP cc_start: 0.6723 (m-30) cc_final: 0.6262 (m-30)
REVERT: A  123 GLU cc_start: 0.6958 (pt0) cc_final: 0.5993 (pt0)
REVERT: A  241 GLU cc_start: 0.6535 (mt-10) cc_final: 0.6303 (mt-10)
REVERT: B   25 CYS cc_start: 0.7178 (m) cc_final: 0.6676 (m)
REVERT: B  135 VAL cc_start: 0.8461 (t) cc_final: 0.8203 (p)
REVERT: B  245 SER cc_start: 0.7960 (p) cc_final: 0.7547 (p)
REVERT: G   13 ARG cc_start: 0.7198 (tmt-80) cc_final: 0.6615 (tmt-80)
REVERT: R  207 LYS cc_start: 0.7849 (tmtt) cc_final: 0.7540 (tmtt)
REVERT: R  250 TRP cc_start: 0.7126 (p-90) cc_final: 0.6650 (p-90)
REVERT: R  262 MET cc_start: 0.6038 (ppp) cc_final: 0.5696 (ppp)
REVERT: R  284 LYS cc_start: 0.7464 (tptp) cc_final: 0.7083 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 259
  average time/residue: 0.1220
  time to fit residues: 40.5367
Evaluate side-chains
  242 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    0.0060
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.1980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
B 155 ASN
B 220 GLN
B 266 HIS
B 340 ASN
** N  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  40 GLN
N  85 ASN
R  65 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.144331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.126426 restraints weight = 12463.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 2.25
r_work: 0.3529 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3362 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.1124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8619  Z= 0.145
  Angle     :  0.565   6.973  11677  Z= 0.302
  Chirality :  0.042   0.175   1322
  Planarity :  0.005   0.067   1475
  Dihedral  :  4.121  18.600   1147
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 10.29 %
    Favored  : 88.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.26), residues: 1054
  helix:  2.28 (0.24), residues: 451
  sheet:  0.24 (0.36), residues: 220
  loop : -0.95 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 251 
 TYR   0.009   0.001   TYR A 194 
 PHE   0.023   0.001   PHE R   9 
 TRP   0.020   0.001   TRP A  99 
 HIS   0.004   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8617)
  covalent geometry    : angle       0.56446 (11673)
  SS BOND              : bond        0.00339 (    2)
  SS BOND              : angle       1.80852 (    4)
  hydrogen bonds       : bond        0.04726 (  463)
  hydrogen bonds       : angle       4.52180 ( 1338)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 237
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.8205 (tp30) cc_final: 0.7702 (tp30)
REVERT: A   29 ASP cc_start: 0.7714 (t0) cc_final: 0.7399 (t0)
REVERT: A   42 LEU cc_start: 0.8233 (mt) cc_final: 0.8023 (mt)
REVERT: A   74 GLU cc_start: 0.7872 (pt0) cc_final: 0.7275 (pt0)
REVERT: A  123 GLU cc_start: 0.7636 (pt0) cc_final: 0.7141 (pt0)
REVERT: A  241 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7233 (mt-10)
REVERT: A  245 ASP cc_start: 0.7466 (t0) cc_final: 0.7255 (t0)
REVERT: B   68 ARG cc_start: 0.8451 (ttt180) cc_final: 0.8175 (ttt90)
REVERT: B   88 ASN cc_start: 0.7965 (m110) cc_final: 0.7663 (m-40)
REVERT: B  212 ASP cc_start: 0.7993 (t0) cc_final: 0.7765 (t0)
REVERT: B  315 VAL cc_start: 0.8221 (t) cc_final: 0.7997 (p)
REVERT: G   13 ARG cc_start: 0.7658 (tmt-80) cc_final: 0.6938 (tmt-80)
REVERT: R  207 LYS cc_start: 0.8120 (tmtt) cc_final: 0.7746 (tmtt)
REVERT: R  247 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.7308 (tmm)
REVERT: R  250 TRP cc_start: 0.7525 (p-90) cc_final: 0.7198 (p-90)
REVERT: R  262 MET cc_start: 0.6724 (ppp) cc_final: 0.6200 (ppp)
REVERT: R  284 LYS cc_start: 0.8271 (tptp) cc_final: 0.7890 (tptp)
  outliers start: 9
  outliers final: 7
  residues processed: 240
  average time/residue: 0.1170
  time to fit residues: 36.2753
Evaluate side-chains
  234 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 226
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain R residue  119 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  244 SER
Chi-restraints excluded: chain R residue  247 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 95 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 99 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 102 optimal weight:    1.9990
   chunk 93 optimal weight:    0.1980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  19 ASN
A 133 ASN
B  88 ASN
R  86 ASN
R 148 ASN
R 224 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.142909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.125008 restraints weight = 12447.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 2.25
r_work: 0.3508 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3341 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8619  Z= 0.174
  Angle     :  0.563   6.727  11677  Z= 0.297
  Chirality :  0.043   0.151   1322
  Planarity :  0.004   0.056   1475
  Dihedral  :  4.162  18.043   1147
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 13.98 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.26), residues: 1054
  helix:  2.22 (0.24), residues: 452
  sheet:  0.30 (0.36), residues: 218
  loop : -1.05 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  19 
 TYR   0.011   0.001   TYR A 194 
 PHE   0.022   0.002   PHE R   9 
 TRP   0.022   0.002   TRP A  99 
 HIS   0.003   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 8617)
  covalent geometry    : angle       0.56213 (11673)
  SS BOND              : bond        0.00344 (    2)
  SS BOND              : angle       1.41289 (    4)
  hydrogen bonds       : bond        0.04710 (  463)
  hydrogen bonds       : angle       4.33120 ( 1338)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 245
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.8245 (tp30) cc_final: 0.7773 (tp30)
REVERT: A   29 ASP cc_start: 0.7780 (t0) cc_final: 0.7406 (t0)
REVERT: A   74 GLU cc_start: 0.7872 (pt0) cc_final: 0.7316 (pt0)
REVERT: A  123 GLU cc_start: 0.7563 (pt0) cc_final: 0.7177 (pt0)
REVERT: A  160 LYS cc_start: 0.8297 (ptpp) cc_final: 0.7900 (mtmm)
REVERT: A  241 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7277 (mt-10)
REVERT: A  245 ASP cc_start: 0.7380 (t0) cc_final: 0.7143 (t0)
REVERT: B   88 ASN cc_start: 0.7960 (m-40) cc_final: 0.7607 (m-40)
REVERT: B  118 ASP cc_start: 0.7651 (t70) cc_final: 0.7133 (t0)
REVERT: B  212 ASP cc_start: 0.8002 (t0) cc_final: 0.7719 (t0)
REVERT: B  262 MET cc_start: 0.7702 (tpt) cc_final: 0.7437 (tpt)
REVERT: B  315 VAL cc_start: 0.8216 (t) cc_final: 0.7993 (p)
REVERT: B  320 VAL cc_start: 0.8258 (t) cc_final: 0.7908 (p)
REVERT: G   13 ARG cc_start: 0.7624 (tmt-80) cc_final: 0.6905 (tmt-80)
REVERT: N   60 SER cc_start: 0.8311 (m) cc_final: 0.7761 (p)
REVERT: R  207 LYS cc_start: 0.8221 (tmtt) cc_final: 0.7805 (tmtt)
REVERT: R  250 TRP cc_start: 0.7630 (p-90) cc_final: 0.7264 (p-90)
REVERT: R  262 MET cc_start: 0.6776 (ppp) cc_final: 0.6277 (ppp)
REVERT: R  284 LYS cc_start: 0.8312 (tptp) cc_final: 0.7912 (tptp)
REVERT: R  287 LYS cc_start: 0.8036 (tppp) cc_final: 0.7567 (tppp)
  outliers start: 20
  outliers final: 14
  residues processed: 253
  average time/residue: 0.1224
  time to fit residues: 39.8373
Evaluate side-chains
  252 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 238
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  119 LEU
Chi-restraints excluded: chain R residue  178 THR
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  244 SER
Chi-restraints excluded: chain R residue  267 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 93 optimal weight:    0.0670
   chunk 69 optimal weight:    0.7980
   chunk 68 optimal weight:    0.0040
   chunk 56 optimal weight:    0.0170
   chunk 95 optimal weight:    0.6980
   chunk 92 optimal weight:    4.9990
   chunk 18 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   overall best weight:    0.2768

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

Flipped N/Q/H residues before XYZ refinement:
A  85 HIS
R  31 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.145153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.127145 restraints weight = 12662.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3678 rms_B_bonded: 2.28
r_work: 0.3543 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.1746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8619  Z= 0.111
  Angle     :  0.522  10.871  11677  Z= 0.275
  Chirality :  0.040   0.133   1322
  Planarity :  0.004   0.050   1475
  Dihedral  :  4.002  20.613   1147
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.56 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 15.17 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.17 (0.26), residues: 1054
  helix:  2.50 (0.24), residues: 450
  sheet:  0.27 (0.35), residues: 220
  loop : -1.06 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 197 
 TYR   0.008   0.001   TYR A 194 
 PHE   0.023   0.001   PHE R   9 
 TRP   0.018   0.001   TRP A  99 
 HIS   0.003   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 8617)
  covalent geometry    : angle       0.52140 (11673)
  SS BOND              : bond        0.00272 (    2)
  SS BOND              : angle       1.89246 (    4)
  hydrogen bonds       : bond        0.04013 (  463)
  hydrogen bonds       : angle       4.10890 ( 1338)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 243
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.7838 (tp30) cc_final: 0.7415 (tp30)
REVERT: A   74 GLU cc_start: 0.7637 (pt0) cc_final: 0.7180 (pt0)
REVERT: A  123 GLU cc_start: 0.7274 (pt0) cc_final: 0.6921 (pt0)
REVERT: A  160 LYS cc_start: 0.8164 (ptpp) cc_final: 0.7822 (mtmm)
REVERT: A  198 ASP cc_start: 0.7618 (t0) cc_final: 0.7236 (m-30)
REVERT: A  241 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6884 (mt-10)
REVERT: A  245 ASP cc_start: 0.7095 (t0) cc_final: 0.6660 (t0)
REVERT: B   88 ASN cc_start: 0.7651 (m-40) cc_final: 0.7447 (m110)
REVERT: B  188 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7368 (mmm)
REVERT: B  197 ARG cc_start: 0.7834 (mmm160) cc_final: 0.7404 (mmm160)
REVERT: B  212 ASP cc_start: 0.7777 (t0) cc_final: 0.7450 (t0)
REVERT: B  304 ARG cc_start: 0.7958 (mtp180) cc_final: 0.7570 (ttm-80)
REVERT: B  315 VAL cc_start: 0.8113 (t) cc_final: 0.7905 (p)
REVERT: N   60 SER cc_start: 0.8167 (m) cc_final: 0.7705 (p)
REVERT: R   17 PHE cc_start: 0.7999 (t80) cc_final: 0.7709 (t80)
REVERT: R  109 LYS cc_start: 0.7771 (mmmm) cc_final: 0.7231 (mmmm)
REVERT: R  207 LYS cc_start: 0.8040 (tmtt) cc_final: 0.7613 (tmtt)
REVERT: R  262 MET cc_start: 0.6716 (ppp) cc_final: 0.6210 (ppp)
REVERT: R  284 LYS cc_start: 0.8049 (tptp) cc_final: 0.7661 (tptp)
REVERT: R  287 LYS cc_start: 0.7829 (tppp) cc_final: 0.7360 (tppp)
  outliers start: 27
  outliers final: 17
  residues processed: 254
  average time/residue: 0.1142
  time to fit residues: 37.9191
Evaluate side-chains
  255 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 237
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue  101 GLN
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain R residue   62 LEU
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue   92 ASN
Chi-restraints excluded: chain R residue  119 LEU
Chi-restraints excluded: chain R residue  168 LEU
Chi-restraints excluded: chain R residue  178 THR
Chi-restraints excluded: chain R residue  244 SER
Chi-restraints excluded: chain R residue  267 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 95 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 71 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 49 optimal weight:    0.1980
   chunk 103 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.142969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.124830 restraints weight = 12521.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 2.25
r_work: 0.3512 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3346 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8619  Z= 0.167
  Angle     :  0.558  12.567  11677  Z= 0.291
  Chirality :  0.042   0.142   1322
  Planarity :  0.004   0.047   1475
  Dihedral  :  4.111  19.102   1147
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.75 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 18.53 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.26), residues: 1054
  helix:  2.40 (0.24), residues: 450
  sheet:  0.33 (0.35), residues: 218
  loop : -1.15 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  19 
 TYR   0.012   0.001   TYR A 194 
 PHE   0.022   0.001   PHE R   9 
 TRP   0.019   0.002   TRP A  99 
 HIS   0.003   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 8617)
  covalent geometry    : angle       0.55755 (11673)
  SS BOND              : bond        0.00363 (    2)
  SS BOND              : angle       1.50254 (    4)
  hydrogen bonds       : bond        0.04425 (  463)
  hydrogen bonds       : angle       4.17275 ( 1338)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 253
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.8264 (tp30) cc_final: 0.7863 (tp30)
REVERT: A   74 GLU cc_start: 0.7867 (pt0) cc_final: 0.7358 (pt0)
REVERT: A   78 GLN cc_start: 0.7838 (pt0) cc_final: 0.7588 (pt0)
REVERT: A  123 GLU cc_start: 0.7573 (pt0) cc_final: 0.7213 (pt0)
REVERT: A  160 LYS cc_start: 0.8263 (ptpp) cc_final: 0.7928 (mtmm)
REVERT: A  198 ASP cc_start: 0.7981 (t0) cc_final: 0.7602 (m-30)
REVERT: A  241 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7238 (mt-10)
REVERT: A  245 ASP cc_start: 0.7378 (t0) cc_final: 0.7163 (t0)
REVERT: B   68 ARG cc_start: 0.8491 (ttt180) cc_final: 0.8225 (ttt90)
REVERT: B   88 ASN cc_start: 0.7963 (m-40) cc_final: 0.7704 (m-40)
REVERT: B  125 ASN cc_start: 0.8481 (t0) cc_final: 0.8215 (t0)
REVERT: B  188 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7731 (mmm)
REVERT: B  197 ARG cc_start: 0.8079 (mmm160) cc_final: 0.7578 (mmm160)
REVERT: B  212 ASP cc_start: 0.8039 (t0) cc_final: 0.7630 (t0)
REVERT: B  304 ARG cc_start: 0.8270 (mtp180) cc_final: 0.7811 (ttm-80)
REVERT: B  315 VAL cc_start: 0.8261 (t) cc_final: 0.8041 (p)
REVERT: B  320 VAL cc_start: 0.8217 (t) cc_final: 0.7869 (p)
REVERT: N   60 SER cc_start: 0.8290 (m) cc_final: 0.7862 (p)
REVERT: R   17 PHE cc_start: 0.8155 (t80) cc_final: 0.7922 (t80)
REVERT: R  207 LYS cc_start: 0.8311 (tmtt) cc_final: 0.7870 (tmtt)
REVERT: R  250 TRP cc_start: 0.7483 (p-90) cc_final: 0.7156 (p-90)
REVERT: R  262 MET cc_start: 0.6843 (ppp) cc_final: 0.6349 (ppp)
REVERT: R  281 TRP cc_start: 0.8364 (t60) cc_final: 0.8100 (t60)
REVERT: R  284 LYS cc_start: 0.8318 (tptp) cc_final: 0.7946 (tptp)
REVERT: R  287 LYS cc_start: 0.8044 (tppp) cc_final: 0.7657 (tppp)
  outliers start: 29
  outliers final: 20
  residues processed: 265
  average time/residue: 0.1220
  time to fit residues: 41.6444
Evaluate side-chains
  268 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 247
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LYS
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue  101 GLN
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  240 LYS
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain N residue  126 THR
Chi-restraints excluded: chain R residue   33 ILE
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue  119 LEU
Chi-restraints excluded: chain R residue  133 LEU
Chi-restraints excluded: chain R residue  168 LEU
Chi-restraints excluded: chain R residue  244 SER
Chi-restraints excluded: chain R residue  267 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 102 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9980
   chunk 59 optimal weight:    0.6980
   chunk 30 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 36 optimal weight:    0.3980
   chunk 85 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 101 GLN
** B  17 GLN ** 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 = 0.3906 r_free = 0.3906 target = 0.143553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.125610 restraints weight = 12439.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 2.26
r_work: 0.3516 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8619  Z= 0.148
  Angle     :  0.551  12.548  11677  Z= 0.287
  Chirality :  0.041   0.136   1322
  Planarity :  0.004   0.046   1475
  Dihedral  :  4.085  17.791   1147
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.56 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 19.18 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.26), residues: 1054
  helix:  2.43 (0.24), residues: 450
  sheet:  0.35 (0.35), residues: 218
  loop : -1.11 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B  19 
 TYR   0.010   0.001   TYR A 194 
 PHE   0.023   0.001   PHE R   9 
 TRP   0.019   0.001   TRP A  99 
 HIS   0.003   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8617)
  covalent geometry    : angle       0.55074 (11673)
  SS BOND              : bond        0.00384 (    2)
  SS BOND              : angle       1.21486 (    4)
  hydrogen bonds       : bond        0.04243 (  463)
  hydrogen bonds       : angle       4.09164 ( 1338)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 234
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.7878 (tp30) cc_final: 0.7450 (tp30)
REVERT: A   29 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7407 (m-30)
REVERT: A   55 GLN cc_start: 0.7197 (OUTLIER) cc_final: 0.6813 (tt0)
REVERT: A   57 ARG cc_start: 0.7709 (tpp80) cc_final: 0.7353 (tpp80)
REVERT: A   74 GLU cc_start: 0.7624 (pt0) cc_final: 0.7174 (pt0)
REVERT: A  123 GLU cc_start: 0.7307 (pt0) cc_final: 0.6976 (pt0)
REVERT: A  198 ASP cc_start: 0.7719 (t0) cc_final: 0.7350 (m-30)
REVERT: A  241 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6860 (mt-10)
REVERT: A  245 ASP cc_start: 0.7138 (t0) cc_final: 0.6779 (t0)
REVERT: B   68 ARG cc_start: 0.8400 (ttt180) cc_final: 0.8135 (ttt90)
REVERT: B   88 ASN cc_start: 0.7759 (m-40) cc_final: 0.7490 (m-40)
REVERT: B  125 ASN cc_start: 0.8365 (t0) cc_final: 0.8059 (t0)
REVERT: B  188 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7400 (mmm)
REVERT: B  197 ARG cc_start: 0.7895 (mmm160) cc_final: 0.7421 (mmm160)
REVERT: B  212 ASP cc_start: 0.7828 (t0) cc_final: 0.7334 (t0)
REVERT: B  315 VAL cc_start: 0.8177 (t) cc_final: 0.7971 (p)
REVERT: B  320 VAL cc_start: 0.8094 (t) cc_final: 0.7761 (p)
REVERT: N   60 SER cc_start: 0.8117 (m) cc_final: 0.7744 (p)
REVERT: N  109 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.7209 (m-80)
REVERT: R  109 LYS cc_start: 0.7837 (mmmm) cc_final: 0.7378 (mmmm)
REVERT: R  207 LYS cc_start: 0.8083 (tmtt) cc_final: 0.7624 (tmtt)
REVERT: R  244 SER cc_start: 0.7406 (OUTLIER) cc_final: 0.7092 (p)
REVERT: R  262 MET cc_start: 0.6692 (ppp) cc_final: 0.6243 (ppp)
REVERT: R  284 LYS cc_start: 0.8115 (tptp) cc_final: 0.7708 (tptp)
REVERT: R  287 LYS cc_start: 0.7852 (tppp) cc_final: 0.7468 (tppp)
  outliers start: 30
  outliers final: 19
  residues processed: 247
  average time/residue: 0.1205
  time to fit residues: 38.0902
Evaluate side-chains
  260 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 236
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LYS
Chi-restraints excluded: chain A residue   29 ASP
Chi-restraints excluded: chain A residue   30 LYS
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue  101 GLN
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain N residue   79 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain R residue   29 LEU
Chi-restraints excluded: chain R residue   33 ILE
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue  114 SER
Chi-restraints excluded: chain R residue  119 LEU
Chi-restraints excluded: chain R residue  168 LEU
Chi-restraints excluded: chain R residue  244 SER
Chi-restraints excluded: chain R residue  267 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 103 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 101 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.142582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.124556 restraints weight = 12560.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 2.26
r_work: 0.3505 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8619  Z= 0.181
  Angle     :  0.576  13.662  11677  Z= 0.299
  Chirality :  0.042   0.135   1322
  Planarity :  0.004   0.046   1475
  Dihedral  :  4.153  18.367   1147
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.75 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 19.61 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.26), residues: 1054
  helix:  2.40 (0.24), residues: 449
  sheet:  0.35 (0.35), residues: 218
  loop : -1.15 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B  19 
 TYR   0.011   0.001   TYR A 194 
 PHE   0.023   0.001   PHE R   9 
 TRP   0.019   0.002   TRP A  99 
 HIS   0.003   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 8617)
  covalent geometry    : angle       0.57553 (11673)
  SS BOND              : bond        0.00379 (    2)
  SS BOND              : angle       1.22915 (    4)
  hydrogen bonds       : bond        0.04469 (  463)
  hydrogen bonds       : angle       4.14453 ( 1338)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 243
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.7907 (tp30) cc_final: 0.7485 (tp30)
REVERT: A   55 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6830 (tt0)
REVERT: A   57 ARG cc_start: 0.7754 (tpp80) cc_final: 0.7403 (tpp80)
REVERT: A   74 GLU cc_start: 0.7647 (pt0) cc_final: 0.7192 (pt0)
REVERT: A   78 GLN cc_start: 0.7734 (pt0) cc_final: 0.7516 (pt0)
REVERT: A   96 ARG cc_start: 0.7431 (ptt180) cc_final: 0.7166 (ptt180)
REVERT: A  123 GLU cc_start: 0.7329 (pt0) cc_final: 0.6985 (pt0)
REVERT: A  129 LYS cc_start: 0.8078 (ttmm) cc_final: 0.7877 (ttmm)
REVERT: A  198 ASP cc_start: 0.7741 (t0) cc_final: 0.7341 (m-30)
REVERT: A  241 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6878 (mt-10)
REVERT: A  245 ASP cc_start: 0.7150 (t0) cc_final: 0.6800 (t0)
REVERT: B   68 ARG cc_start: 0.8382 (ttt180) cc_final: 0.8120 (ttt90)
REVERT: B   88 ASN cc_start: 0.7797 (m-40) cc_final: 0.7526 (m-40)
REVERT: B  125 ASN cc_start: 0.8354 (t0) cc_final: 0.8028 (t0)
REVERT: B  188 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7399 (mmm)
REVERT: B  197 ARG cc_start: 0.7892 (mmm160) cc_final: 0.7402 (mmm160)
REVERT: B  212 ASP cc_start: 0.7847 (t0) cc_final: 0.7279 (t0)
REVERT: B  320 VAL cc_start: 0.8114 (t) cc_final: 0.7791 (p)
REVERT: N   60 SER cc_start: 0.8125 (m) cc_final: 0.7748 (p)
REVERT: N  109 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.7267 (m-80)
REVERT: R   17 PHE cc_start: 0.8083 (t80) cc_final: 0.7857 (t80)
REVERT: R  109 LYS cc_start: 0.7849 (mmmm) cc_final: 0.7402 (mmmm)
REVERT: R  207 LYS cc_start: 0.8071 (tmtt) cc_final: 0.7612 (tmtt)
REVERT: R  244 SER cc_start: 0.7407 (OUTLIER) cc_final: 0.7117 (p)
REVERT: R  262 MET cc_start: 0.6677 (ppp) cc_final: 0.6247 (ppp)
REVERT: R  284 LYS cc_start: 0.8145 (tptp) cc_final: 0.7754 (tptp)
REVERT: R  287 LYS cc_start: 0.7875 (tppp) cc_final: 0.7496 (tppp)
  outliers start: 28
  outliers final: 20
  residues processed: 257
  average time/residue: 0.1129
  time to fit residues: 37.3596
Evaluate side-chains
  261 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 237
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LYS
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain N residue    3 VAL
Chi-restraints excluded: chain N residue   79 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain R residue   29 LEU
Chi-restraints excluded: chain R residue   33 ILE
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue  114 SER
Chi-restraints excluded: chain R residue  119 LEU
Chi-restraints excluded: chain R residue  168 LEU
Chi-restraints excluded: chain R residue  244 SER
Chi-restraints excluded: chain R residue  267 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 91 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 93 optimal weight:    0.2980
   chunk 25 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
R 112 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.143157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.125120 restraints weight = 12507.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 2.26
r_work: 0.3511 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8619  Z= 0.161
  Angle     :  0.583  13.124  11677  Z= 0.300
  Chirality :  0.042   0.140   1322
  Planarity :  0.004   0.046   1475
  Dihedral  :  4.146  18.103   1147
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.75 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 20.69 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.26), residues: 1054
  helix:  2.42 (0.24), residues: 450
  sheet:  0.36 (0.35), residues: 218
  loop : -1.13 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B  19 
 TYR   0.010   0.001   TYR N  61 
 PHE   0.023   0.001   PHE R   9 
 TRP   0.017   0.002   TRP A  99 
 HIS   0.003   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 8617)
  covalent geometry    : angle       0.58248 (11673)
  SS BOND              : bond        0.00399 (    2)
  SS BOND              : angle       1.15601 (    4)
  hydrogen bonds       : bond        0.04330 (  463)
  hydrogen bonds       : angle       4.09954 ( 1338)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 235
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.7912 (tp30) cc_final: 0.7493 (tp30)
REVERT: A   55 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6832 (tt0)
REVERT: A   74 GLU cc_start: 0.7608 (pt0) cc_final: 0.7143 (pt0)
REVERT: A   78 GLN cc_start: 0.7705 (pt0) cc_final: 0.7481 (pt0)
REVERT: A   96 ARG cc_start: 0.7393 (ptt180) cc_final: 0.7119 (ptt180)
REVERT: A  123 GLU cc_start: 0.7361 (pt0) cc_final: 0.6996 (pt0)
REVERT: A  198 ASP cc_start: 0.7724 (t0) cc_final: 0.7335 (m-30)
REVERT: A  241 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6849 (mt-10)
REVERT: A  245 ASP cc_start: 0.7142 (t0) cc_final: 0.6796 (t0)
REVERT: B   68 ARG cc_start: 0.8380 (ttt180) cc_final: 0.8127 (ttt90)
REVERT: B   88 ASN cc_start: 0.7801 (m-40) cc_final: 0.7523 (m-40)
REVERT: B  125 ASN cc_start: 0.8363 (t0) cc_final: 0.8037 (t0)
REVERT: B  188 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7417 (mmm)
REVERT: B  197 ARG cc_start: 0.7894 (mmm160) cc_final: 0.7408 (mmm160)
REVERT: B  212 ASP cc_start: 0.7856 (t0) cc_final: 0.7282 (t0)
REVERT: B  320 VAL cc_start: 0.8120 (t) cc_final: 0.7790 (p)
REVERT: N   60 SER cc_start: 0.8128 (m) cc_final: 0.7756 (p)
REVERT: N  109 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.7199 (m-80)
REVERT: R  109 LYS cc_start: 0.7848 (mmmm) cc_final: 0.7420 (mmmm)
REVERT: R  207 LYS cc_start: 0.8080 (tmtt) cc_final: 0.7619 (tmtt)
REVERT: R  244 SER cc_start: 0.7435 (OUTLIER) cc_final: 0.7131 (p)
REVERT: R  262 MET cc_start: 0.6646 (ppp) cc_final: 0.6243 (ppp)
REVERT: R  284 LYS cc_start: 0.8124 (tptp) cc_final: 0.7723 (tptp)
REVERT: R  287 LYS cc_start: 0.7899 (tppp) cc_final: 0.7547 (tppp)
  outliers start: 31
  outliers final: 20
  residues processed: 251
  average time/residue: 0.1203
  time to fit residues: 38.5151
Evaluate side-chains
  259 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 235
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LYS
Chi-restraints excluded: chain A residue   30 LYS
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue    3 VAL
Chi-restraints excluded: chain N residue   79 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain R residue   29 LEU
Chi-restraints excluded: chain R residue   33 ILE
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue  112 ASN
Chi-restraints excluded: chain R residue  119 LEU
Chi-restraints excluded: chain R residue  121 LEU
Chi-restraints excluded: chain R residue  168 LEU
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  244 SER
Chi-restraints excluded: chain R residue  267 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 73 optimal weight:    0.7980
   chunk 12 optimal weight:    0.4980
   chunk 58 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0870
   chunk 50 optimal weight:    0.8980
   chunk 56 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 94 optimal weight:    0.5980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A 147 ASN
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
R 112 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.144110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.125873 restraints weight = 12471.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 2.27
r_work: 0.3516 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.2170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8619  Z= 0.142
  Angle     :  0.576  14.319  11677  Z= 0.295
  Chirality :  0.041   0.141   1322
  Planarity :  0.004   0.046   1475
  Dihedral  :  4.105  17.698   1147
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.75 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 20.69 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.26), residues: 1054
  helix:  2.46 (0.24), residues: 450
  sheet:  0.38 (0.35), residues: 218
  loop : -1.10 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B  19 
 TYR   0.009   0.001   TYR A 194 
 PHE   0.023   0.001   PHE R   9 
 TRP   0.017   0.001   TRP A  99 
 HIS   0.003   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8617)
  covalent geometry    : angle       0.57620 (11673)
  SS BOND              : bond        0.00389 (    2)
  SS BOND              : angle       1.06502 (    4)
  hydrogen bonds       : bond        0.04184 (  463)
  hydrogen bonds       : angle       4.05988 ( 1338)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 235
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 ARG cc_start: 0.6944 (ttm-80) cc_final: 0.6642 (mtm-85)
REVERT: A   23 GLU cc_start: 0.7892 (tp30) cc_final: 0.7474 (tp30)
REVERT: A   29 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7375 (m-30)
REVERT: A   55 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6825 (tt0)
REVERT: A   74 GLU cc_start: 0.7632 (pt0) cc_final: 0.7177 (pt0)
REVERT: A   96 ARG cc_start: 0.7350 (ptt180) cc_final: 0.7061 (ptt180)
REVERT: A  123 GLU cc_start: 0.7325 (pt0) cc_final: 0.6978 (pt0)
REVERT: A  198 ASP cc_start: 0.7719 (t0) cc_final: 0.7329 (m-30)
REVERT: A  241 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6865 (mt-10)
REVERT: A  245 ASP cc_start: 0.7116 (t0) cc_final: 0.6773 (t0)
REVERT: B   68 ARG cc_start: 0.8361 (ttt180) cc_final: 0.8102 (ttt90)
REVERT: B   88 ASN cc_start: 0.7770 (m-40) cc_final: 0.7507 (m-40)
REVERT: B  125 ASN cc_start: 0.8359 (t0) cc_final: 0.8012 (t0)
REVERT: B  188 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7466 (mmm)
REVERT: B  197 ARG cc_start: 0.7912 (mmm160) cc_final: 0.7416 (mmm160)
REVERT: B  212 ASP cc_start: 0.7847 (t0) cc_final: 0.7256 (t0)
REVERT: B  320 VAL cc_start: 0.8109 (t) cc_final: 0.7776 (p)
REVERT: N   60 SER cc_start: 0.8118 (m) cc_final: 0.7758 (p)
REVERT: N  109 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.7230 (m-80)
REVERT: R   17 PHE cc_start: 0.8058 (t80) cc_final: 0.7848 (t80)
REVERT: R  109 LYS cc_start: 0.7863 (mmmm) cc_final: 0.7442 (mmmm)
REVERT: R  207 LYS cc_start: 0.8075 (tmtt) cc_final: 0.7611 (tmtt)
REVERT: R  244 SER cc_start: 0.7440 (OUTLIER) cc_final: 0.7108 (p)
REVERT: R  262 MET cc_start: 0.6627 (ppp) cc_final: 0.6240 (ppp)
REVERT: R  281 TRP cc_start: 0.8216 (t60) cc_final: 0.8009 (t60)
REVERT: R  284 LYS cc_start: 0.8147 (tptp) cc_final: 0.7776 (tptp)
REVERT: R  287 LYS cc_start: 0.7906 (tppp) cc_final: 0.7639 (tppp)
  outliers start: 30
  outliers final: 21
  residues processed: 249
  average time/residue: 0.1285
  time to fit residues: 40.7152
Evaluate side-chains
  257 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 231
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ASP
Chi-restraints excluded: chain A residue   30 LYS
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue    3 VAL
Chi-restraints excluded: chain N residue   79 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  126 THR
Chi-restraints excluded: chain R residue   29 LEU
Chi-restraints excluded: chain R residue   33 ILE
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue  114 SER
Chi-restraints excluded: chain R residue  119 LEU
Chi-restraints excluded: chain R residue  121 LEU
Chi-restraints excluded: chain R residue  168 LEU
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  244 SER
Chi-restraints excluded: chain R residue  267 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 93 optimal weight:    0.0030
   chunk 2 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 78 optimal weight:    6.9990
   chunk 14 optimal weight:    0.6980
   chunk 94 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
R 112 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.143751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.125596 restraints weight = 12508.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 2.27
r_work: 0.3519 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8619  Z= 0.149
  Angle     :  0.592  14.401  11677  Z= 0.303
  Chirality :  0.042   0.141   1322
  Planarity :  0.004   0.047   1475
  Dihedral  :  4.097  17.630   1147
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.85 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 21.45 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.26), residues: 1054
  helix:  2.48 (0.24), residues: 450
  sheet:  0.36 (0.35), residues: 218
  loop : -1.11 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  19 
 TYR   0.010   0.001   TYR A 194 
 PHE   0.024   0.001   PHE R   9 
 TRP   0.016   0.001   TRP A  99 
 HIS   0.003   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 8617)
  covalent geometry    : angle       0.59140 (11673)
  SS BOND              : bond        0.00399 (    2)
  SS BOND              : angle       1.06790 (    4)
  hydrogen bonds       : bond        0.04220 (  463)
  hydrogen bonds       : angle       4.05951 ( 1338)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 225
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 ARG cc_start: 0.6936 (ttm-80) cc_final: 0.6626 (mtm-85)
REVERT: A   23 GLU cc_start: 0.7911 (tp30) cc_final: 0.7516 (tp30)
REVERT: A   55 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6815 (tt0)
REVERT: A   74 GLU cc_start: 0.7598 (pt0) cc_final: 0.7166 (pt0)
REVERT: A   96 ARG cc_start: 0.7369 (ptt180) cc_final: 0.7081 (ptt180)
REVERT: A  123 GLU cc_start: 0.7325 (pt0) cc_final: 0.6986 (pt0)
REVERT: A  198 ASP cc_start: 0.7721 (t0) cc_final: 0.7334 (m-30)
REVERT: A  241 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6872 (mt-10)
REVERT: A  245 ASP cc_start: 0.7129 (t0) cc_final: 0.6801 (t0)
REVERT: B   23 LYS cc_start: 0.8697 (tmtt) cc_final: 0.8490 (tmtt)
REVERT: B   68 ARG cc_start: 0.8395 (ttt180) cc_final: 0.8142 (ttt90)
REVERT: B   88 ASN cc_start: 0.7765 (m-40) cc_final: 0.7518 (m-40)
REVERT: B  125 ASN cc_start: 0.8376 (t0) cc_final: 0.8032 (t0)
REVERT: B  188 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7451 (mmm)
REVERT: B  197 ARG cc_start: 0.7914 (mmm160) cc_final: 0.7427 (mmm160)
REVERT: B  212 ASP cc_start: 0.7842 (t0) cc_final: 0.7267 (t0)
REVERT: B  320 VAL cc_start: 0.8116 (t) cc_final: 0.7784 (p)
REVERT: N   60 SER cc_start: 0.8116 (m) cc_final: 0.7770 (p)
REVERT: N  109 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7286 (m-80)
REVERT: R   82 ILE cc_start: 0.6646 (mm) cc_final: 0.6289 (mm)
REVERT: R  109 LYS cc_start: 0.7854 (mmmm) cc_final: 0.7449 (mmmm)
REVERT: R  207 LYS cc_start: 0.8090 (tmtt) cc_final: 0.7632 (tmtt)
REVERT: R  244 SER cc_start: 0.7460 (OUTLIER) cc_final: 0.7132 (p)
REVERT: R  262 MET cc_start: 0.6641 (ppp) cc_final: 0.6252 (ppp)
REVERT: R  284 LYS cc_start: 0.8144 (tptp) cc_final: 0.7763 (tptp)
REVERT: R  287 LYS cc_start: 0.7967 (tppp) cc_final: 0.7674 (tppp)
  outliers start: 25
  outliers final: 21
  residues processed: 241
  average time/residue: 0.1332
  time to fit residues: 40.6636
Evaluate side-chains
  248 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 223
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LYS
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue    3 VAL
Chi-restraints excluded: chain N residue   79 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  126 THR
Chi-restraints excluded: chain R residue   29 LEU
Chi-restraints excluded: chain R residue   33 ILE
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue  112 ASN
Chi-restraints excluded: chain R residue  119 LEU
Chi-restraints excluded: chain R residue  121 LEU
Chi-restraints excluded: chain R residue  168 LEU
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  244 SER
Chi-restraints excluded: chain R residue  267 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 92 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
R 112 ASN
R 148 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.142852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.124700 restraints weight = 12400.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 2.26
r_work: 0.3508 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8619  Z= 0.180
  Angle     :  0.603  14.243  11677  Z= 0.309
  Chirality :  0.042   0.147   1322
  Planarity :  0.004   0.049   1475
  Dihedral  :  4.165  18.246   1147
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.75 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 21.45 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.26), residues: 1054
  helix:  2.44 (0.24), residues: 450
  sheet:  0.36 (0.35), residues: 218
  loop : -1.17 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B  19 
 TYR   0.012   0.001   TYR N  61 
 PHE   0.023   0.002   PHE R   9 
 TRP   0.016   0.002   TRP A  99 
 HIS   0.003   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 8617)
  covalent geometry    : angle       0.60308 (11673)
  SS BOND              : bond        0.00428 (    2)
  SS BOND              : angle       1.12191 (    4)
  hydrogen bonds       : bond        0.04422 (  463)
  hydrogen bonds       : angle       4.09859 ( 1338)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2202.36 seconds
wall clock time: 38 minutes 26.33 seconds (2306.33 seconds total)