Starting phenix.real_space_refine
on Sun Apr  5 04:03:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wcm_32424/04_2026/7wcm_32424.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wcm_32424/04_2026/7wcm_32424.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wcm_32424/04_2026/7wcm_32424.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wcm_32424/04_2026/7wcm_32424.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wcm_32424/04_2026/7wcm_32424.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wcm_32424/04_2026/7wcm_32424.map"
  }
  resolution = 2.33
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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      57      5.16       5
     C    5222      2.51       5
     N    1435      2.21       5
     O    1518      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8232
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1947
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 228}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2606
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2606
          Classifications: {'peptide': 339}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "C"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "N"
      Number of atoms: 983
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 983
          Classifications: {'peptide': 129}
          Link IDs: {'PTRANS': 5, 'TRANS': 123}
    Chain: "R"
      Number of atoms: 2240
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2240
          Classifications: {'peptide': 289}
          Link IDs: {'PTRANS': 9, 'TRANS': 279}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'8VP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.88, per 1000 atoms: 0.23
  Number of scatterers: 8232
  At special positions: 0
  Unit cell: (81.696, 102.12, 131.054, 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      57     16.00
     O    1518      8.00
     N    1435      7.00
     C    5222      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  78 " - pdb=" SG  CYS R 155 " 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: 0.84
  Conformation dependent library (CDL) restraints added in 338.6 milliseconds
  

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1958

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 10 sheets defined
      45.0% alpha, 20.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 40
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 234 through 239
      removed outlier: 3.663A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.749A  pdb=" N   ALA A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 283
      removed outlier: 4.035A  pdb=" N   ARG A 283 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 312 through 318
      removed outlier: 3.551A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.572A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 391
      removed outlier: 3.550A  pdb=" N   ARG A 373 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 37
    Processing helix  chain 'B' and resid 40 through 45
      removed outlier: 3.577A  pdb=" N   ILE B  44 " --> pdb=" O   THR B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 48
      No H-bonds generated for 'chain 'B' and resid 46 through 48'
    Processing helix  chain 'C' and resid 9 through 23
      removed outlier: 3.831A  pdb=" N   LYS C  14 " --> pdb=" O   ALA C  10 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 45 through 48
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
      removed outlier: 3.646A  pdb=" N   LYS N  65 " --> pdb=" O   GLY N  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 62 through 65'
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 6 through 36
      removed outlier: 3.699A  pdb=" N   VAL R  25 " --> pdb=" O   THR R  21 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 38 through 60
      removed outlier: 3.583A  pdb=" N   CYS R  42 " --> pdb=" O   GLY R  38 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 62 through 68
      removed outlier: 3.781A  pdb=" N   SER R  68 " --> pdb=" O   ASP R  64 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 74 through 109
      removed outlier: 3.966A  pdb=" N   VAL R  85 " --> pdb=" O   ARG R  81 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   THR R  86 " --> pdb=" O   MET R  82 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 109 through 117
    Processing helix  chain 'R' and resid 118 through 139
    Processing helix  chain 'R' and resid 140 through 143
    Processing helix  chain 'R' and resid 163 through 173
    Processing helix  chain 'R' and resid 173 through 210
      removed outlier: 3.614A  pdb=" N   ALA R 177 " --> pdb=" O   GLY R 173 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 221 through 236
    Processing helix  chain 'R' and resid 238 through 251
    Processing helix  chain 'R' and resid 255 through 263
      removed outlier: 4.182A  pdb=" N   VAL R 259 " --> pdb=" O   HIS R 255 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLU R 261 " --> pdb=" O   TYR R 257 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 263 through 280
      removed outlier: 3.723A  pdb=" N   LEU R 267 " --> pdb=" O   TYR R 263 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   SER R 272 " --> pdb=" O   GLY R 268 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   LEU R 273 " --> pdb=" O   VAL R 269 " (cutoff:3.500A)
      Proline residue:  R 276  - end of helix
    Processing helix  chain 'R' and resid 283 through 300
      removed outlier: 3.687A  pdb=" N   LEU R 295 " --> pdb=" O   TYR R 291 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLY R 296 " --> pdb=" O   HIS R 292 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL R 297 " --> pdb=" O   MET R 293 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LYS R 298 " --> pdb=" O   ALA R 294 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 4.449A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 62
      removed outlier: 6.798A  pdb=" N   ILE B 349 " --> pdb=" O   ARG B  59 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   THR B  61 " --> pdb=" O   LEU B 347 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   LEU B 347 " --> pdb=" O   THR B  61 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 74
      removed outlier: 3.637A  pdb=" N   ALA B  71 " --> pdb=" O   ALA B  84 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   LEU B  90 " --> pdb=" O   ALA B 103 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   ALA B 103 " --> pdb=" O   LEU B  90 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   ILE B  92 " --> pdb=" O   VAL B 101 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 116
      removed outlier: 6.967A  pdb=" N   GLY B 126 " --> pdb=" O   MET B 112 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   CYS B 114 " --> pdb=" O   ALA B 124 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   ALA B 124 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   TYR B 116 " --> pdb=" O   TYR B 122 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   TYR B 122 " --> pdb=" O   TYR B 116 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   GLY B 127 " --> pdb=" O   ILE B 131 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   ILE B 131 " --> pdb=" O   GLY B 127 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   CYS B 132 " --> pdb=" O   GLU B 149 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   GLU B 149 " --> pdb=" O   CYS B 132 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   ILE B 134 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ARG B 145 " --> pdb=" O   ASN B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 157 through 162
      removed outlier: 6.732A  pdb=" N   SER B 171 " --> pdb=" O   SER B 158 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   CYS B 160 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   VAL B 169 " --> pdb=" O   CYS B 160 " (cutoff:3.500A)
      removed outlier: 4.963A  pdb=" N   PHE B 162 " --> pdb=" O   GLN B 167 " (cutoff:3.500A)
      removed outlier: 7.423A  pdb=" N   GLN B 167 " --> pdb=" O   PHE B 162 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ILE B 168 " --> pdb=" O   TRP B 180 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   ASP B 181 " --> pdb=" O   GLN B 187 " (cutoff:3.500A)
      removed outlier: 6.006A  pdb=" N   GLN B 187 " --> pdb=" O   ASP B 181 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 198 through 203
      removed outlier: 3.559A  pdb=" N   SER B 200 " --> pdb=" O   GLY B 213 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   SER B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLN B 231 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   ASP B 223 " --> pdb=" O   CYS B 229 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   CYS B 229 " --> pdb=" O   ASP B 223 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 245
      removed outlier: 6.639A  pdb=" N   CYS B 261 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   THR B 274 " --> pdb=" O   CYS B 261 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   LEU B 263 " --> pdb=" O   LEU B 272 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLN B 270 " --> pdb=" O   ASP B 265 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 284 through 289
      removed outlier: 3.740A  pdb=" N   SER B 286 " --> pdb=" O   GLY B 299 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   ASP B 309 " --> pdb=" O   ARG B 315 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   ARG B 315 " --> pdb=" O   ASP B 309 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.790A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    449 hydrogen bonds defined for protein.
    1269 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: 1.45

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2690
        1.34 -     1.46: 1962
        1.46 -     1.58: 3666
        1.58 -     1.70: 0
        1.70 -     1.82: 82
  Bond restraints: 8400
  Sorted by residual:
  bond pdb=" C20 8VP R 401 "
       pdb=" N17 8VP R 401 "
    ideal  model  delta    sigma   weight residual
    1.357  1.473 -0.116 2.00e-02 2.50e+03 3.39e+01
  bond pdb=" C8  8VP R 401 "
       pdb=" C9  8VP R 401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.579 -0.089 2.00e-02 2.50e+03 1.99e+01
  bond pdb=" C9  8VP R 401 "
       pdb=" N13 8VP R 401 "
    ideal  model  delta    sigma   weight residual
    1.378  1.448 -0.070 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" C29 8VP R 401 "
       pdb=" N28 8VP R 401 "
    ideal  model  delta    sigma   weight residual
    1.344  1.401 -0.057 2.00e-02 2.50e+03 8.23e+00
  bond pdb=" C3  8VP R 401 "
       pdb=" N28 8VP R 401 "
    ideal  model  delta    sigma   weight residual
    1.423  1.478 -0.055 2.00e-02 2.50e+03 7.62e+00
  ... (remaining 8395 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 11151
        1.80 -     3.60: 175
        3.60 -     5.40: 36
        5.40 -     7.20: 4
        7.20 -     9.00: 3
  Bond angle restraints: 11369
  Sorted by residual:
  angle pdb=" N   PHE N 108 "
        pdb=" CA  PHE N 108 "
        pdb=" C   PHE N 108 "
      ideal   model   delta    sigma   weight residual
     111.24  115.14   -3.90 1.29e+00 6.01e-01 9.12e+00
  angle pdb=" C9  8VP R 401 "
        pdb=" C8  8VP R 401 "
        pdb=" O7  8VP R 401 "
      ideal   model   delta    sigma   weight residual
     107.91  116.91   -9.00 3.00e+00 1.11e-01 8.99e+00
  angle pdb=" C16 8VP R 401 "
        pdb=" N17 8VP R 401 "
        pdb=" C18 8VP R 401 "
      ideal   model   delta    sigma   weight residual
     116.58  107.78    8.80 3.00e+00 1.11e-01 8.60e+00
  angle pdb=" C   PRO R 144 "
        pdb=" N   MET R 145 "
        pdb=" CA  MET R 145 "
      ideal   model   delta    sigma   weight residual
     121.54  126.54   -5.00 1.91e+00 2.74e-01 6.84e+00
  angle pdb=" CA  ASP A 310 "
        pdb=" CB  ASP A 310 "
        pdb=" CG  ASP A 310 "
      ideal   model   delta    sigma   weight residual
     112.60  115.17   -2.57 1.00e+00 1.00e+00 6.60e+00
  ... (remaining 11364 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 4536
       17.93 -    35.85: 399
       35.85 -    53.78: 49
       53.78 -    71.70: 15
       71.70 -    89.63: 13
  Dihedral angle restraints: 5012
    sinusoidal: 1980
      harmonic: 3032
  Sorted by residual:
  dihedral pdb=" CA  ASP A 310 "
           pdb=" C   ASP A 310 "
           pdb=" N   TYR A 311 "
           pdb=" CA  TYR A 311 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.84   27.16     0      5.00e+00 4.00e-02 2.95e+01
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.68  -24.32     0      5.00e+00 4.00e-02 2.36e+01
  dihedral pdb=" CA  GLN B  86 "
           pdb=" C   GLN B  86 "
           pdb=" N   ASP B  87 "
           pdb=" CA  ASP B  87 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.36   18.64     0      5.00e+00 4.00e-02 1.39e+01
  ... (remaining 5009 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 852
       0.036 -    0.072: 303
       0.072 -    0.108: 91
       0.108 -    0.144: 32
       0.144 -    0.180: 2
  Chirality restraints: 1280
  Sorted by residual:
  chirality pdb=" CA  VAL N  37 "
            pdb=" N   VAL N  37 "
            pdb=" C   VAL N  37 "
            pdb=" CB  VAL N  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.13e-01
  chirality pdb=" CA  TYR B  70 "
            pdb=" N   TYR B  70 "
            pdb=" C   TYR B  70 "
            pdb=" CB  TYR B  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.22e-01
  chirality pdb=" CA  ASP A 310 "
            pdb=" N   ASP A 310 "
            pdb=" C   ASP A 310 "
            pdb=" CB  ASP A 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.17e-01
  ... (remaining 1277 not shown)

  Planarity restraints: 1448
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  70 "   -0.027 2.00e-02 2.50e+03   2.03e-02 8.28e+00
        pdb=" CG  TYR B  70 "    0.049 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  70 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  70 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  70 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  70 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  70 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B  70 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 246 "    0.034 5.00e-02 4.00e+02   5.16e-02 4.26e+00
        pdb=" N   PRO B 247 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO B 247 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 247 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 183 "    0.009 2.00e-02 2.50e+03   1.84e-02 3.38e+00
        pdb=" C   PHE R 183 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   PHE R 183 "    0.012 2.00e-02 2.50e+03
        pdb=" N   PHE R 184 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1445 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2044
        2.80 -     3.33: 7580
        3.33 -     3.85: 13284
        3.85 -     4.38: 15798
        4.38 -     4.90: 27122
  Nonbonded interactions: 65828
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A  29 "
            pdb=" OD1 ASP A  33 "
     model   vdw
     2.281 3.120
  nonbonded pdb=" NH1 ARG A 228 "
            pdb=" OD1 ASP B 197 "
     model   vdw
     2.301 3.120
  nonbonded pdb=" O   GLN R 148 "
            pdb=" NZ  LYS R 152 "
     model   vdw
     2.306 3.120
  nonbonded pdb=" O   TYR B  96 "
            pdb=" OG1 THR B  97 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" OD1 ASN A 292 "
            pdb=" N   LYS A 293 "
     model   vdw
     2.356 3.120
  ... (remaining 65823 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:             2.030
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.710
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
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   0.116   8402  Z= 0.178
  Angle     :  0.607   8.996  11373  Z= 0.329
  Chirality :  0.043   0.180   1280
  Planarity :  0.004   0.052   1448
  Dihedral  : 14.074  89.628   3048
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  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:  1.05 (0.26), residues: 1031
  helix:  1.81 (0.27), residues: 411
  sheet:  1.03 (0.35), residues: 208
  loop : -0.61 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 230 
 TYR   0.049   0.002   TYR B  70 
 PHE   0.014   0.001   PHE A 212 
 TRP   0.022   0.002   TRP B  93 
 HIS   0.015   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8400)
  covalent geometry    : angle       0.60724 (11369)
  SS BOND              : bond        0.00567 (    2)
  SS BOND              : angle       0.88776 (    4)
  hydrogen bonds       : bond        0.14907 (  449)
  hydrogen bonds       : angle       5.78490 ( 1269)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.336 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.8692
  time to fit residues: 118.8365
Evaluate side-chains
  120 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    8.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.0040
   chunk 100 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   overall best weight:    2.1198

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  27 ASN
B 279 ASN
R 109 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.160237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.107946 restraints weight = 7701.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 1.65
r_work: 0.3022 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.1044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8402  Z= 0.158
  Angle     :  0.612   9.710  11373  Z= 0.337
  Chirality :  0.045   0.194   1280
  Planarity :  0.004   0.051   1448
  Dihedral  :  6.314  70.755   1164
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  6.66 %
    Favored  : 91.65 %
  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:  1.30 (0.26), residues: 1031
  helix:  2.18 (0.26), residues: 418
  sheet:  1.04 (0.35), residues: 212
  loop : -0.68 (0.29), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  38 
 TYR   0.016   0.002   TYR A 339 
 PHE   0.015   0.002   PHE A 212 
 TRP   0.021   0.002   TRP A 234 
 HIS   0.012   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8400)
  covalent geometry    : angle       0.61164 (11369)
  SS BOND              : bond        0.00971 (    2)
  SS BOND              : angle       1.00108 (    4)
  hydrogen bonds       : bond        0.06597 (  449)
  hydrogen bonds       : angle       4.57987 ( 1269)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A  300 LYS cc_start: 0.6799 (OUTLIER) cc_final: 0.6345 (mtmt)
REVERT: A  314 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6650 (mt-10)
REVERT: C   29 LYS cc_start: 0.8335 (mmtm) cc_final: 0.7969 (mtpp)
REVERT: N    3 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7751 (tp-100)
REVERT: R  261 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6083 (mm-30)
  outliers start: 15
  outliers final: 6
  residues processed: 125
  average time/residue: 0.8420
  time to fit residues: 109.8752
Evaluate side-chains
  127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue  115 LYS
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  190 LYS
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  259 VAL
Chi-restraints excluded: chain R residue  261 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 55 optimal weight:    6.9990
   chunk 49 optimal weight:    0.0970
   chunk 35 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  27 ASN
N   5 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.163768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.113397 restraints weight = 7767.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 1.82
r_work: 0.3090 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.1227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8402  Z= 0.108
  Angle     :  0.497   7.564  11373  Z= 0.274
  Chirality :  0.041   0.198   1280
  Planarity :  0.004   0.050   1448
  Dihedral  :  5.721  63.393   1164
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  9.48 %
    Favored  : 89.16 %
  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:  1.59 (0.27), residues: 1031
  helix:  2.60 (0.26), residues: 417
  sheet:  0.90 (0.34), residues: 220
  loop : -0.57 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  38 
 TYR   0.013   0.001   TYR A 339 
 PHE   0.013   0.001   PHE A 212 
 TRP   0.015   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 8400)
  covalent geometry    : angle       0.49703 (11369)
  SS BOND              : bond        0.00532 (    2)
  SS BOND              : angle       0.69686 (    4)
  hydrogen bonds       : bond        0.04822 (  449)
  hydrogen bonds       : angle       4.17644 ( 1269)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8414 (tp40) cc_final: 0.8011 (tp-100)
REVERT: A  314 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6676 (mt-10)
REVERT: B   70 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.7652 (m-80)
REVERT: C   29 LYS cc_start: 0.8060 (mmtm) cc_final: 0.7749 (mtpp)
REVERT: R  115 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7530 (ttpp)
  outliers start: 12
  outliers final: 2
  residues processed: 124
  average time/residue: 0.8823
  time to fit residues: 114.0892
Evaluate side-chains
  119 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 114
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain R residue  115 LYS
Chi-restraints excluded: chain R residue  190 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 99 optimal weight:    0.0980
   chunk 2 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0470
   chunk 30 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.0282

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  27 ASN
N   3 GLN
N   5 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.162443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.110546 restraints weight = 7927.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 1.68
r_work: 0.3059 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2926 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.1268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8402  Z= 0.115
  Angle     :  0.516   9.577  11373  Z= 0.282
  Chirality :  0.042   0.195   1280
  Planarity :  0.004   0.050   1448
  Dihedral  :  5.689  61.729   1164
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  9.82 %
    Favored  : 88.49 %
  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:  1.63 (0.27), residues: 1031
  helix:  2.68 (0.26), residues: 417
  sheet:  0.97 (0.34), residues: 219
  loop : -0.64 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  38 
 TYR   0.013   0.001   TYR A 339 
 PHE   0.014   0.001   PHE A 212 
 TRP   0.017   0.001   TRP A 234 
 HIS   0.002   0.001   HIS B 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 8400)
  covalent geometry    : angle       0.51543 (11369)
  SS BOND              : bond        0.00613 (    2)
  SS BOND              : angle       0.71596 (    4)
  hydrogen bonds       : bond        0.05081 (  449)
  hydrogen bonds       : angle       4.19582 ( 1269)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8437 (tp40) cc_final: 0.8051 (tp-100)
REVERT: A  300 LYS cc_start: 0.6751 (OUTLIER) cc_final: 0.6275 (mtmt)
REVERT: A  314 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6666 (mt-10)
REVERT: B   70 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.8269 (m-80)
REVERT: C   29 LYS cc_start: 0.8082 (mmtm) cc_final: 0.7720 (mtpp)
REVERT: R  115 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7479 (ttpp)
  outliers start: 15
  outliers final: 3
  residues processed: 123
  average time/residue: 0.8306
  time to fit residues: 106.7950
Evaluate side-chains
  121 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain N residue  105 ARG
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue  115 LYS
Chi-restraints excluded: chain R residue  190 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 43 optimal weight:    0.3980
   chunk 42 optimal weight:    4.9990
   chunk 16 optimal weight:    0.4980
   chunk 51 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 99 optimal weight:    9.9990
   chunk 37 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9990
   chunk 63 optimal weight:    9.9990
   chunk 10 optimal weight:    8.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 390 GLN
B  27 ASN
N   3 GLN
N   5 GLN
R 197 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.159558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.112015 restraints weight = 7780.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 1.77
r_work: 0.3027 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.1290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8402  Z= 0.156
  Angle     :  0.605   9.460  11373  Z= 0.331
  Chirality :  0.044   0.197   1280
  Planarity :  0.004   0.051   1448
  Dihedral  :  5.949  58.571   1164
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 10.27 %
    Favored  : 88.04 %
  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:  1.47 (0.26), residues: 1031
  helix:  2.46 (0.26), residues: 418
  sheet:  1.15 (0.35), residues: 211
  loop : -0.76 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  38 
 TYR   0.015   0.002   TYR A 339 
 PHE   0.016   0.002   PHE A 212 
 TRP   0.022   0.002   TRP A 234 
 HIS   0.004   0.001   HIS B  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 8400)
  covalent geometry    : angle       0.60470 (11369)
  SS BOND              : bond        0.01043 (    2)
  SS BOND              : angle       0.89085 (    4)
  hydrogen bonds       : bond        0.06374 (  449)
  hydrogen bonds       : angle       4.48319 ( 1269)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8493 (tp40) cc_final: 0.8186 (tp-100)
REVERT: A  300 LYS cc_start: 0.6781 (OUTLIER) cc_final: 0.6273 (mtmt)
REVERT: A  314 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6671 (mt-10)
REVERT: B   70 TYR cc_start: 0.9154 (OUTLIER) cc_final: 0.8379 (m-80)
REVERT: C   29 LYS cc_start: 0.8327 (mmtm) cc_final: 0.7955 (mtpp)
REVERT: C   32 LYS cc_start: 0.7833 (tttm) cc_final: 0.7615 (mtpm)
  outliers start: 15
  outliers final: 8
  residues processed: 131
  average time/residue: 0.8433
  time to fit residues: 115.2283
Evaluate side-chains
  124 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue  115 LYS
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  166 VAL
Chi-restraints excluded: chain R residue  190 LYS
Chi-restraints excluded: chain R residue  259 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 53 optimal weight:    9.9990
   chunk 77 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 29 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 55 optimal weight:    4.9990
   chunk 93 optimal weight:    8.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  27 ASN
N   3 GLN
N   5 GLN
R 197 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.161283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.109665 restraints weight = 7727.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 1.64
r_work: 0.3045 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.1322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8402  Z= 0.124
  Angle     :  0.539   8.261  11373  Z= 0.295
  Chirality :  0.042   0.197   1280
  Planarity :  0.004   0.051   1448
  Dihedral  :  5.683  55.577   1164
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 10.72 %
    Favored  : 87.47 %
  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:  1.62 (0.26), residues: 1031
  helix:  2.62 (0.26), residues: 418
  sheet:  1.07 (0.34), residues: 217
  loop : -0.66 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  38 
 TYR   0.013   0.001   TYR A 339 
 PHE   0.014   0.001   PHE A 212 
 TRP   0.018   0.002   TRP A 234 
 HIS   0.002   0.001   HIS R 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 8400)
  covalent geometry    : angle       0.53850 (11369)
  SS BOND              : bond        0.00743 (    2)
  SS BOND              : angle       0.74612 (    4)
  hydrogen bonds       : bond        0.05345 (  449)
  hydrogen bonds       : angle       4.27019 ( 1269)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8430 (tp40) cc_final: 0.8089 (tp-100)
REVERT: A  300 LYS cc_start: 0.6702 (OUTLIER) cc_final: 0.6204 (mtmt)
REVERT: A  314 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6674 (mt-10)
REVERT: B   70 TYR cc_start: 0.9148 (OUTLIER) cc_final: 0.8269 (m-80)
REVERT: C   29 LYS cc_start: 0.8137 (mmtm) cc_final: 0.7766 (mtpp)
REVERT: R  115 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7450 (tppp)
  outliers start: 16
  outliers final: 6
  residues processed: 126
  average time/residue: 0.8620
  time to fit residues: 113.2032
Evaluate side-chains
  124 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue  115 LYS
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  166 VAL
Chi-restraints excluded: chain R residue  190 LYS
Chi-restraints excluded: chain R residue  236 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 63 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0030
   chunk 96 optimal weight:    0.6980
   chunk 48 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 87 optimal weight:    0.1980
   chunk 59 optimal weight:    0.8980
   chunk 98 optimal weight:    9.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  27 ASN
N   3 GLN
N   5 GLN
R 197 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.164919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.113571 restraints weight = 7936.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 1.68
r_work: 0.3105 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8402  Z= 0.102
  Angle     :  0.487   7.867  11373  Z= 0.265
  Chirality :  0.041   0.197   1280
  Planarity :  0.003   0.050   1448
  Dihedral  :  5.330  51.588   1164
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 11.29 %
    Favored  : 87.47 %
  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:  1.77 (0.27), residues: 1031
  helix:  2.82 (0.26), residues: 417
  sheet:  0.98 (0.34), residues: 220
  loop : -0.56 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  38 
 TYR   0.013   0.001   TYR A 339 
 PHE   0.013   0.001   PHE A 212 
 TRP   0.014   0.001   TRP B 308 
 HIS   0.001   0.000   HIS R 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00193 ( 8400)
  covalent geometry    : angle       0.48713 (11369)
  SS BOND              : bond        0.00511 (    2)
  SS BOND              : angle       0.55676 (    4)
  hydrogen bonds       : bond        0.04338 (  449)
  hydrogen bonds       : angle       4.04134 ( 1269)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A  300 LYS cc_start: 0.6758 (OUTLIER) cc_final: 0.6259 (mtmt)
REVERT: B   70 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.7822 (m-80)
REVERT: C   29 LYS cc_start: 0.7935 (mmtm) cc_final: 0.7610 (mmtp)
  outliers start: 11
  outliers final: 3
  residues processed: 123
  average time/residue: 0.8503
  time to fit residues: 109.2636
Evaluate side-chains
  114 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 109
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain R residue  190 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 81 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 87 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   chunk 61 optimal weight:    0.8980
   chunk 94 optimal weight:    1.9990
   chunk 100 optimal weight:    7.9990
   chunk 56 optimal weight:    3.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  27 ASN
N   3 GLN
R 197 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.160296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.108288 restraints weight = 7820.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 1.64
r_work: 0.3027 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8402  Z= 0.148
  Angle     :  0.586  10.014  11373  Z= 0.319
  Chirality :  0.044   0.196   1280
  Planarity :  0.004   0.050   1448
  Dihedral  :  5.713  50.997   1164
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 11.63 %
    Favored  : 86.57 %
  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:  1.60 (0.26), residues: 1031
  helix:  2.59 (0.26), residues: 419
  sheet:  1.20 (0.34), residues: 211
  loop : -0.71 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  38 
 TYR   0.014   0.002   TYR A 339 
 PHE   0.015   0.002   PHE A 212 
 TRP   0.020   0.002   TRP A 234 
 HIS   0.004   0.001   HIS B  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8400)
  covalent geometry    : angle       0.58621 (11369)
  SS BOND              : bond        0.00985 (    2)
  SS BOND              : angle       0.84768 (    4)
  hydrogen bonds       : bond        0.05986 (  449)
  hydrogen bonds       : angle       4.37723 ( 1269)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A  300 LYS cc_start: 0.6730 (OUTLIER) cc_final: 0.6222 (mtmt)
REVERT: A  314 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6685 (mt-10)
REVERT: B   70 TYR cc_start: 0.9154 (OUTLIER) cc_final: 0.8323 (m-80)
  outliers start: 16
  outliers final: 5
  residues processed: 116
  average time/residue: 0.8286
  time to fit residues: 100.2437
Evaluate side-chains
  119 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  190 LYS
Chi-restraints excluded: chain R residue  236 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 63 optimal weight:   10.0000
   chunk 100 optimal weight:    5.9990
   chunk 99 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   chunk 88 optimal weight:    5.9990
   chunk 30 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 72 optimal weight:    6.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
B  27 ASN
N   3 GLN
N   5 GLN
R 197 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.157607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.105330 restraints weight = 7773.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 1.64
r_work: 0.2980 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   8402  Z= 0.236
  Angle     :  0.735  11.368  11373  Z= 0.401
  Chirality :  0.049   0.202   1280
  Planarity :  0.005   0.051   1448
  Dihedral  :  6.178  51.351   1164
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 11.63 %
    Favored  : 86.68 %
  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: 1031
  helix:  2.02 (0.25), residues: 419
  sheet:  1.06 (0.34), residues: 222
  loop : -0.79 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  63 
 TYR   0.017   0.003   TYR R 134 
 PHE   0.018   0.002   PHE A 212 
 TRP   0.026   0.003   TRP A 234 
 HIS   0.009   0.002   HIS B  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 ( 8400)
  covalent geometry    : angle       0.73529 (11369)
  SS BOND              : bond        0.01600 (    2)
  SS BOND              : angle       1.15285 (    4)
  hydrogen bonds       : bond        0.07887 (  449)
  hydrogen bonds       : angle       4.79074 ( 1269)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8491 (tp40) cc_final: 0.8229 (tp-100)
REVERT: A  300 LYS cc_start: 0.6825 (OUTLIER) cc_final: 0.6313 (mtmt)
REVERT: A  314 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6684 (mt-10)
REVERT: B   70 TYR cc_start: 0.9182 (OUTLIER) cc_final: 0.8592 (m-80)
  outliers start: 15
  outliers final: 9
  residues processed: 123
  average time/residue: 0.8553
  time to fit residues: 109.6623
Evaluate side-chains
  125 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  166 VAL
Chi-restraints excluded: chain R residue  190 LYS
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  259 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 34 optimal weight:    8.9990
   chunk 41 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 35 optimal weight:    6.9990
   chunk 8 optimal weight:    0.8980
   chunk 19 optimal weight:    6.9990
   chunk 94 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  27 ASN
B 277 HIS
N   3 GLN
N   5 GLN
R 197 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.160614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.108828 restraints weight = 7740.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 1.63
r_work: 0.3033 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.1437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8402  Z= 0.138
  Angle     :  0.580   9.521  11373  Z= 0.316
  Chirality :  0.044   0.201   1280
  Planarity :  0.004   0.051   1448
  Dihedral  :  5.821  49.297   1164
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 11.96 %
    Favored  : 86.68 %
  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:  1.47 (0.26), residues: 1031
  helix:  2.47 (0.26), residues: 418
  sheet:  1.17 (0.35), residues: 209
  loop : -0.78 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  38 
 TYR   0.014   0.001   TYR A 339 
 PHE   0.015   0.001   PHE A 212 
 TRP   0.019   0.002   TRP A 234 
 HIS   0.005   0.001   HIS B 277 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 8400)
  covalent geometry    : angle       0.57999 (11369)
  SS BOND              : bond        0.00894 (    2)
  SS BOND              : angle       0.82590 (    4)
  hydrogen bonds       : bond        0.05831 (  449)
  hydrogen bonds       : angle       4.40258 ( 1269)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8458 (tp40) cc_final: 0.8104 (tp-100)
REVERT: A  300 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.6207 (mtmt)
REVERT: A  314 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6676 (mt-10)
REVERT: A  367 VAL cc_start: 0.2951 (OUTLIER) cc_final: 0.2637 (m)
REVERT: B   70 TYR cc_start: 0.9151 (OUTLIER) cc_final: 0.8344 (m-80)
REVERT: C   29 LYS cc_start: 0.8266 (mmtm) cc_final: 0.7939 (mtpp)
REVERT: N  105 ARG cc_start: 0.7658 (mtt180) cc_final: 0.7368 (mtm180)
REVERT: R  261 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6753 (mm-30)
  outliers start: 12
  outliers final: 4
  residues processed: 116
  average time/residue: 0.8518
  time to fit residues: 103.2256
Evaluate side-chains
  119 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  190 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 79 optimal weight:    6.9990
   chunk 72 optimal weight:   10.0000
   chunk 73 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 43 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  27 ASN
B 277 HIS
N   3 GLN
N   5 GLN
R 197 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.158981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.106892 restraints weight = 7821.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 1.64
r_work: 0.3006 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2870 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.1487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8402  Z= 0.173
  Angle     :  0.643  10.245  11373  Z= 0.350
  Chirality :  0.046   0.202   1280
  Planarity :  0.004   0.051   1448
  Dihedral  :  5.974  49.078   1164
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 11.74 %
    Favored  : 86.68 %
  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:  1.36 (0.26), residues: 1031
  helix:  2.34 (0.25), residues: 418
  sheet:  1.19 (0.34), residues: 207
  loop : -0.84 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  38 
 TYR   0.015   0.002   TYR A 339 
 PHE   0.015   0.002   PHE A 212 
 TRP   0.022   0.002   TRP A 234 
 HIS   0.006   0.001   HIS B 277 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 8400)
  covalent geometry    : angle       0.64258 (11369)
  SS BOND              : bond        0.01213 (    2)
  SS BOND              : angle       0.98641 (    4)
  hydrogen bonds       : bond        0.06738 (  449)
  hydrogen bonds       : angle       4.58542 ( 1269)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4594.42 seconds
wall clock time: 78 minutes 38.71 seconds (4718.71 seconds total)