Starting phenix.real_space_refine
on Fri Jul 25 22:42:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wcm_32424/07_2025/7wcm_32424.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wcm_32424/07_2025/7wcm_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wcm_32424/07_2025/7wcm_32424.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wcm_32424/07_2025/7wcm_32424.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wcm_32424/07_2025/7wcm_32424.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wcm_32424/07_2025/7wcm_32424.cif"
  }
  resolution = 2.33
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.67, per 1000 atoms: 0.69
  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: 2.50
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.94
  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: 2.46

  Time building geometry restraints manager: 2.79 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:             8.470
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.460
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  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:13.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.630
-------------------------------------------------------------------------------
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 : 3.66
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.022   0.002   TRP B  93 
 HIS   0.015   0.001   HIS A 357 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.049   0.002   TYR B  70 
 ARG   0.002   0.000   ARG B 230 

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

*********************** 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  : 0.903 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 1.6443
  time to fit residues: 225.4852
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  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    5.9990
   chunk 76 optimal weight:    4.9990
   chunk 42 optimal weight:   10.0000
   chunk 26 optimal weight:    0.6980
   chunk 51 optimal weight:    8.9990
   chunk 40 optimal weight:    5.9990
   chunk 79 optimal weight:    0.5980
   chunk 30 optimal weight:    5.9990
   chunk 48 optimal weight:    8.9990
   chunk 58 optimal weight:    5.9990
   chunk 91 optimal weight:    5.9990
   overall best weight:    3.6586

-------------------------------------------------------------------------------
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 = 0.3812 r_free = 0.3812 target = 0.158139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.107737 restraints weight = 7622.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 1.78
r_work: 0.2980 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.1243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8402  Z= 0.215
  Angle     :  0.710  10.608  11373  Z= 0.390
  Chirality :  0.048   0.191   1280
  Planarity :  0.005   0.053   1448
  Dihedral  :  6.594  71.434   1164
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  :  6.66 %
    Favored  : 91.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.26), residues: 1031
  helix:  1.84 (0.25), residues: 419
  sheet:  1.03 (0.35), residues: 210
  loop : -0.81 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP A 234 
 HIS   0.012   0.002   HIS A 357 
 PHE   0.017   0.002   PHE B 245 
 TYR   0.017   0.003   TYR A 339 
 ARG   0.005   0.001   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07816 (  449)
  hydrogen bonds       : angle       4.83335 ( 1269)
  SS BOND              : bond        0.01388 (    2)
  SS BOND              : angle       1.14092 (    4)
  covalent geometry    : bond        0.00469 ( 8400)
  covalent geometry    : angle       0.70938 (11369)

*********************** 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
  137 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.944 
Fit side-chains
REVERT: A  300 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6379 (mtmt)
REVERT: A  314 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6719 (mt-10)
REVERT: R  261 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.5917 (mm-30)
  outliers start: 19
  outliers final: 10
  residues processed: 126
  average time/residue: 1.8595
  time to fit residues: 245.5661
Evaluate side-chains
  128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 1.507 
-------------------------------------------------------------------------------
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  279 ASN
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain R residue   11 LEU
Chi-restraints excluded: chain R residue   42 CYS
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 45 optimal weight:    0.0270
   chunk 38 optimal weight:    0.7980
   chunk 94 optimal weight:    4.9990
   chunk 83 optimal weight:    3.9990
   chunk 85 optimal weight:    5.9990
   chunk 81 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 91 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 92 optimal weight:    0.8980
   chunk 41 optimal weight:    6.9990
   overall best weight:    1.7442

-------------------------------------------------------------------------------
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 = 0.3833 r_free = 0.3833 target = 0.160036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.112213 restraints weight = 7839.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 1.77
r_work: 0.3026 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.1176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8402  Z= 0.144
  Angle     :  0.582   9.010  11373  Z= 0.320
  Chirality :  0.044   0.198   1280
  Planarity :  0.004   0.052   1448
  Dihedral  :  6.151  65.227   1164
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  9.03 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.26), residues: 1031
  helix:  2.25 (0.26), residues: 418
  sheet:  1.04 (0.34), residues: 214
  loop : -0.77 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 234 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.014   0.002   TYR A 339 
 ARG   0.004   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06217 (  449)
  hydrogen bonds       : angle       4.51850 ( 1269)
  SS BOND              : bond        0.00859 (    2)
  SS BOND              : angle       0.93933 (    4)
  covalent geometry    : bond        0.00287 ( 8400)
  covalent geometry    : angle       0.58141 (11369)

*********************** 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: 16
    poor density    : 117
  time to evaluate  : 0.941 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8511 (tp40) cc_final: 0.8123 (tp-100)
REVERT: A  300 LYS cc_start: 0.6834 (OUTLIER) cc_final: 0.6367 (mtmt)
REVERT: A  314 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6692 (mt-10)
REVERT: B   70 TYR cc_start: 0.9154 (OUTLIER) cc_final: 0.8434 (m-80)
REVERT: C   29 LYS cc_start: 0.8374 (mmtm) cc_final: 0.8053 (mtpp)
REVERT: R  261 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.5942 (mm-30)
  outliers start: 16
  outliers final: 8
  residues processed: 125
  average time/residue: 1.6433
  time to fit residues: 215.0296
Evaluate side-chains
  127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
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  190 LYS
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  246 ILE
Chi-restraints excluded: chain R residue  259 VAL
Chi-restraints excluded: chain R residue  261 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 57 optimal weight:    6.9990
   chunk 28 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 91 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   chunk 93 optimal weight:   10.0000
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3868 r_free = 0.3868 target = 0.163301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.111391 restraints weight = 7836.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 1.99
r_work: 0.3051 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.1265

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= 0.112
  Angle     :  0.506   7.712  11373  Z= 0.279
  Chirality :  0.041   0.198   1280
  Planarity :  0.004   0.051   1448
  Dihedral  :  5.716  61.753   1164
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  :  9.93 %
    Favored  : 88.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.26), residues: 1031
  helix:  2.61 (0.26), residues: 417
  sheet:  0.99 (0.34), residues: 218
  loop : -0.71 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 234 
 HIS   0.002   0.001   HIS B 102 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.014   0.001   TYR A 339 
 ARG   0.006   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04947 (  449)
  hydrogen bonds       : angle       4.20416 ( 1269)
  SS BOND              : bond        0.00588 (    2)
  SS BOND              : angle       0.73130 (    4)
  covalent geometry    : bond        0.00213 ( 8400)
  covalent geometry    : angle       0.50621 (11369)

*********************** 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
  139 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 0.905 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8406 (tp40) cc_final: 0.8157 (tp40)
REVERT: A  314 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6720 (mt-10)
REVERT: B   70 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.7790 (m-80)
REVERT: C   29 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7792 (mtpp)
REVERT: R  115 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7466 (ttpp)
REVERT: R  261 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.5880 (mm-30)
  outliers start: 17
  outliers final: 4
  residues processed: 129
  average time/residue: 1.6659
  time to fit residues: 224.9994
Evaluate side-chains
  127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue  115 LYS
Chi-restraints excluded: chain R residue  166 VAL
Chi-restraints excluded: chain R residue  190 LYS
Chi-restraints excluded: chain R residue  261 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 4 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 100 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9980
   chunk 65 optimal weight:    7.9990
   chunk 31 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 98 optimal weight:    9.9990
   chunk 82 optimal weight:    8.9990
   overall best weight:    2.9586

-------------------------------------------------------------------------------
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 = 0.3814 r_free = 0.3814 target = 0.158515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.106379 restraints weight = 7730.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 1.64
r_work: 0.2997 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2861 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.1344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8402  Z= 0.186
  Angle     :  0.657  10.959  11373  Z= 0.359
  Chirality :  0.046   0.192   1280
  Planarity :  0.004   0.052   1448
  Dihedral  :  6.119  58.413   1164
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  :  9.48 %
    Favored  : 87.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.26), residues: 1031
  helix:  2.34 (0.26), residues: 413
  sheet:  1.14 (0.35), residues: 211
  loop : -0.83 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 234 
 HIS   0.005   0.001   HIS B  65 
 PHE   0.016   0.002   PHE A 212 
 TYR   0.016   0.002   TYR A 339 
 ARG   0.006   0.001   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07022 (  449)
  hydrogen bonds       : angle       4.64718 ( 1269)
  SS BOND              : bond        0.01274 (    2)
  SS BOND              : angle       1.02785 (    4)
  covalent geometry    : bond        0.00400 ( 8400)
  covalent geometry    : angle       0.65640 (11369)

*********************** 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: 23
    poor density    : 116
  time to evaluate  : 0.945 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8551 (tp40) cc_final: 0.8159 (tp-100)
REVERT: A  300 LYS cc_start: 0.6758 (OUTLIER) cc_final: 0.6253 (mtmt)
REVERT: A  314 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6671 (mt-10)
REVERT: B   70 TYR cc_start: 0.9156 (OUTLIER) cc_final: 0.8404 (m-80)
REVERT: R  261 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.5964 (mm-30)
  outliers start: 23
  outliers final: 11
  residues processed: 128
  average time/residue: 1.8013
  time to fit residues: 241.1763
Evaluate side-chains
  127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
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   11 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
Chi-restraints excluded: chain R residue  246 ILE
Chi-restraints excluded: chain R residue  259 VAL
Chi-restraints excluded: chain R residue  261 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0570
   chunk 73 optimal weight:   10.0000
   chunk 49 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 59 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 80 optimal weight:    9.9990
   chunk 40 optimal weight:    4.9990
   overall best weight:    1.3702

-------------------------------------------------------------------------------
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 = 0.3836 r_free = 0.3836 target = 0.160520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.108793 restraints weight = 7749.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 1.65
r_work: 0.3032 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.1280

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= 0.129
  Angle     :  0.553   9.294  11373  Z= 0.303
  Chirality :  0.043   0.196   1280
  Planarity :  0.004   0.052   1448
  Dihedral  :  5.824  56.552   1164
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 10.50 %
    Favored  : 87.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.26), residues: 1031
  helix:  2.60 (0.26), residues: 412
  sheet:  1.09 (0.34), residues: 213
  loop : -0.73 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 234 
 HIS   0.002   0.001   HIS B 102 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.014   0.001   TYR A 339 
 ARG   0.005   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05622 (  449)
  hydrogen bonds       : angle       4.37052 ( 1269)
  SS BOND              : bond        0.00771 (    2)
  SS BOND              : angle       0.81486 (    4)
  covalent geometry    : bond        0.00253 ( 8400)
  covalent geometry    : angle       0.55324 (11369)

*********************** 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
  134 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 1.044 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8478 (tp40) cc_final: 0.8080 (tp-100)
REVERT: A  300 LYS cc_start: 0.6708 (OUTLIER) cc_final: 0.6216 (mtmt)
REVERT: A  314 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6653 (mt-10)
REVERT: B   70 TYR cc_start: 0.9153 (OUTLIER) cc_final: 0.8282 (m-80)
REVERT: C   29 LYS cc_start: 0.8243 (mmtm) cc_final: 0.8012 (mtpp)
REVERT: C   42 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7129 (tp30)
REVERT: R  261 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.5938 (mm-30)
  outliers start: 19
  outliers final: 8
  residues processed: 123
  average time/residue: 1.7571
  time to fit residues: 226.1967
Evaluate side-chains
  122 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
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 C residue   42 GLU
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  261 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9990
   chunk 96 optimal weight:    0.7980
   chunk 17 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 80 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0170
   chunk 55 optimal weight:    0.9980
   chunk 10 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.9622

-------------------------------------------------------------------------------
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 = 0.3857 r_free = 0.3857 target = 0.162492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.110934 restraints weight = 7836.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 1.65
r_work: 0.3063 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.1367

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= 0.115
  Angle     :  0.523   8.866  11373  Z= 0.284
  Chirality :  0.042   0.195   1280
  Planarity :  0.004   0.051   1448
  Dihedral  :  5.590  52.991   1164
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 11.06 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.26), residues: 1031
  helix:  2.79 (0.26), residues: 411
  sheet:  1.08 (0.34), residues: 217
  loop : -0.69 (0.29), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 234 
 HIS   0.002   0.001   HIS R 204 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.013   0.001   TYR A 339 
 ARG   0.005   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05022 (  449)
  hydrogen bonds       : angle       4.21648 ( 1269)
  SS BOND              : bond        0.00645 (    2)
  SS BOND              : angle       0.71120 (    4)
  covalent geometry    : bond        0.00221 ( 8400)
  covalent geometry    : angle       0.52246 (11369)

*********************** 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: 20
    poor density    : 112
  time to evaluate  : 1.030 
Fit side-chains
REVERT: A  300 LYS cc_start: 0.6683 (OUTLIER) cc_final: 0.6186 (mtmt)
REVERT: A  314 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6674 (mt-10)
REVERT: B   70 TYR cc_start: 0.9141 (OUTLIER) cc_final: 0.8242 (m-80)
REVERT: C   29 LYS cc_start: 0.8166 (mmtm) cc_final: 0.7871 (mtpp)
REVERT: C   42 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7338 (mp0)
REVERT: R  115 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7449 (tppp)
  outliers start: 20
  outliers final: 9
  residues processed: 119
  average time/residue: 1.7346
  time to fit residues: 215.9117
Evaluate side-chains
  124 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  240 ASP
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 C residue   42 GLU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 92 optimal weight:    7.9990
   chunk 83 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 2 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 94 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 100 optimal weight:    4.9990
   chunk 85 optimal weight:    6.9990
   overall best weight:    1.3788

-------------------------------------------------------------------------------
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 = 0.3843 r_free = 0.3843 target = 0.161178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.109244 restraints weight = 7827.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 1.66
r_work: 0.3036 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.1353

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= 0.127
  Angle     :  0.551   8.993  11373  Z= 0.300
  Chirality :  0.042   0.196   1280
  Planarity :  0.004   0.051   1448
  Dihedral  :  5.672  50.982   1164
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 11.63 %
    Favored  : 86.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.26), residues: 1031
  helix:  2.73 (0.26), residues: 411
  sheet:  1.20 (0.34), residues: 211
  loop : -0.75 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 234 
 HIS   0.002   0.001   HIS R 204 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.014   0.001   TYR A 339 
 ARG   0.007   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05516 (  449)
  hydrogen bonds       : angle       4.32237 ( 1269)
  SS BOND              : bond        0.00769 (    2)
  SS BOND              : angle       0.78495 (    4)
  covalent geometry    : bond        0.00252 ( 8400)
  covalent geometry    : angle       0.55086 (11369)

*********************** 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
  130 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 1.020 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8460 (tp40) cc_final: 0.8206 (tp40)
REVERT: A  300 LYS cc_start: 0.6726 (OUTLIER) cc_final: 0.6223 (mtmt)
REVERT: A  314 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6672 (mt-10)
REVERT: B   70 TYR cc_start: 0.9143 (OUTLIER) cc_final: 0.8251 (m-80)
REVERT: C   29 LYS cc_start: 0.8243 (mmtm) cc_final: 0.7940 (mtpp)
REVERT: C   42 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7393 (mp0)
  outliers start: 17
  outliers final: 10
  residues processed: 119
  average time/residue: 1.7212
  time to fit residues: 214.6489
Evaluate side-chains
  124 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
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 C residue   42 GLU
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  236 LEU
Chi-restraints excluded: chain R residue  259 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 92 optimal weight:    2.9990
   chunk 9 optimal weight:    7.9990
   chunk 96 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9980
   chunk 77 optimal weight:    5.9990
   chunk 78 optimal weight:    6.9990
   chunk 63 optimal weight:   10.0000
   chunk 99 optimal weight:    2.9990
   chunk 86 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    2.9988

-------------------------------------------------------------------------------
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 = 0.3812 r_free = 0.3812 target = 0.158450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.106212 restraints weight = 7860.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 1.66
r_work: 0.2993 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2858 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.1436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8402  Z= 0.187
  Angle     :  0.660  10.083  11373  Z= 0.359
  Chirality :  0.046   0.199   1280
  Planarity :  0.004   0.051   1448
  Dihedral  :  6.024  50.590   1164
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 11.74 %
    Favored  : 86.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.26), residues: 1031
  helix:  2.37 (0.25), residues: 412
  sheet:  1.21 (0.34), residues: 211
  loop : -0.82 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 234 
 HIS   0.006   0.001   HIS B  65 
 PHE   0.016   0.002   PHE A 212 
 TYR   0.015   0.002   TYR A 339 
 ARG   0.008   0.001   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07052 (  449)
  hydrogen bonds       : angle       4.64479 ( 1269)
  SS BOND              : bond        0.01308 (    2)
  SS BOND              : angle       1.03665 (    4)
  covalent geometry    : bond        0.00403 ( 8400)
  covalent geometry    : angle       0.65976 (11369)

*********************** 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
  132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 1.711 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8546 (tp40) cc_final: 0.8140 (tp-100)
REVERT: A  300 LYS cc_start: 0.6769 (OUTLIER) cc_final: 0.6265 (mtmt)
REVERT: A  314 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6671 (mt-10)
REVERT: B   70 TYR cc_start: 0.9160 (OUTLIER) cc_final: 0.8484 (m-80)
  outliers start: 18
  outliers final: 10
  residues processed: 122
  average time/residue: 1.9419
  time to fit residues: 248.4610
Evaluate side-chains
  125 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 1.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
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  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 28 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 50 optimal weight:    7.9990
   chunk 65 optimal weight:    0.0770
   chunk 63 optimal weight:   10.0000
   chunk 77 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    1.0140

-------------------------------------------------------------------------------
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 = 0.3851 r_free = 0.3851 target = 0.161920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.109913 restraints weight = 7736.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 1.67
r_work: 0.3051 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2917 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.1372

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= 0.118
  Angle     :  0.535   8.460  11373  Z= 0.291
  Chirality :  0.042   0.197   1280
  Planarity :  0.004   0.051   1448
  Dihedral  :  5.629  48.609   1164
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 12.42 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.26), residues: 1031
  helix:  2.64 (0.26), residues: 418
  sheet:  1.10 (0.34), residues: 217
  loop : -0.75 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 234 
 HIS   0.002   0.001   HIS B 102 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.014   0.001   TYR A 339 
 ARG   0.007   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05177 (  449)
  hydrogen bonds       : angle       4.27666 ( 1269)
  SS BOND              : bond        0.00673 (    2)
  SS BOND              : angle       0.70799 (    4)
  covalent geometry    : bond        0.00227 ( 8400)
  covalent geometry    : angle       0.53477 (11369)

********************** 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
  127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 1.148 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8457 (tp40) cc_final: 0.8187 (tp40)
REVERT: A  300 LYS cc_start: 0.6695 (OUTLIER) cc_final: 0.6209 (mtmt)
REVERT: A  314 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6669 (mt-10)
REVERT: B   70 TYR cc_start: 0.9146 (OUTLIER) cc_final: 0.8272 (m-80)
REVERT: C   29 LYS cc_start: 0.8171 (mmtm) cc_final: 0.7940 (mtpp)
REVERT: N    3 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7948 (tp-100)
REVERT: R  115 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7457 (ttpp)
  outliers start: 14
  outliers final: 8
  residues processed: 118
  average time/residue: 1.7600
  time to fit residues: 217.0714
Evaluate side-chains
  123 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
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    3 GLN
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  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 24 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 86 optimal weight:    0.0270
   chunk 67 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 94 optimal weight:    5.9990
   chunk 96 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.7640

-------------------------------------------------------------------------------
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 = 0.3851 r_free = 0.3851 target = 0.161993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.110069 restraints weight = 7894.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 1.68
r_work: 0.3050 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2917 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.1368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.137   8402  Z= 0.158
  Angle     :  0.908  59.175  11373  Z= 0.538
  Chirality :  0.049   0.932   1280
  Planarity :  0.004   0.051   1448
  Dihedral  :  5.619  48.611   1164
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 12.42 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.26), residues: 1031
  helix:  2.65 (0.26), residues: 418
  sheet:  1.20 (0.34), residues: 211
  loop : -0.79 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 234 
 HIS   0.002   0.001   HIS R 204 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.013   0.001   TYR A 339 
 ARG   0.006   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05174 (  449)
  hydrogen bonds       : angle       4.27818 ( 1269)
  SS BOND              : bond        0.00632 (    2)
  SS BOND              : angle       0.69580 (    4)
  covalent geometry    : bond        0.00309 ( 8400)
  covalent geometry    : angle       0.90841 (11369)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9401.29 seconds
wall clock time: 163 minutes 37.44 seconds (9817.44 seconds total)