Starting phenix.real_space_refine
on Wed Feb 12 16:40:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wcm_32424/02_2025/7wcm_32424.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wcm_32424/02_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_32424/02_2025/7wcm_32424.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wcm_32424/02_2025/7wcm_32424.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wcm_32424/02_2025/7wcm_32424.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wcm_32424/02_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.35, per 1000 atoms: 0.65
  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: 2.38
  Conformation dependent library (CDL) restraints added in 960.3 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: 0.95
  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: 2.35

  Time building geometry restraints manager: 2.72 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:             1.730
  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:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     22.110
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  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:12.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.550
-------------------------------------------------------------------------------
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   8400  Z= 0.236
  Angle     :  0.607   8.996  11369  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 

*********************** 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  : 0.844 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 1.6613
  time to fit residues: 227.9763
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  : 0.889 
-------------------------------------------------------------------------------
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): 0.3169 rms_B_bonded: 1.78
r_work: 0.2977 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
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   8400  Z= 0.303
  Angle     :  0.709  10.608  11369  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 

*********************** 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  : 0.988 
Fit side-chains
REVERT: A  300 LYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6401 (mtmt)
REVERT: A  314 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6723 (mt-10)
REVERT: R  261 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.5926 (mm-30)
  outliers start: 19
  outliers final: 10
  residues processed: 126
  average time/residue: 1.7386
  time to fit residues: 229.3903
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  : 0.893 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 32 optimal weight:    9.9990
   chunk 92 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   overall best weight:    1.5644

-------------------------------------------------------------------------------
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 = 0.3835 r_free = 0.3835 target = 0.160211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.112646 restraints weight = 7852.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 1.81
r_work: 0.3039 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2905 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.1165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8400  Z= 0.178
  Angle     :  0.571   9.022  11369  Z= 0.314
  Chirality :  0.043   0.198   1280
  Planarity :  0.004   0.052   1448
  Dihedral  :  6.126  65.555   1164
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  9.26 %
    Favored  : 89.05 %
  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:  2.29 (0.26), residues: 418
  sheet:  1.05 (0.34), residues: 214
  loop : -0.76 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 234 
 HIS   0.003   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 

*********************** 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: 15
    poor density    : 118
  time to evaluate  : 0.901 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8491 (tp40) cc_final: 0.8099 (tp-100)
REVERT: A  300 LYS cc_start: 0.6825 (OUTLIER) cc_final: 0.6357 (mtmt)
REVERT: A  314 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6678 (mt-10)
REVERT: B   70 TYR cc_start: 0.9139 (OUTLIER) cc_final: 0.7669 (m-80)
REVERT: C   29 LYS cc_start: 0.8325 (mmtm) cc_final: 0.8002 (mtpp)
REVERT: N    3 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7904 (tp-100)
REVERT: R  261 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.5932 (mm-30)
  outliers start: 15
  outliers final: 7
  residues processed: 126
  average time/residue: 1.7466
  time to fit residues: 230.1424
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  : 0.907 
-------------------------------------------------------------------------------
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 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 26 optimal weight:    0.2980
   chunk 2 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 57 optimal weight:    4.9990
   chunk 28 optimal weight:    0.1980
   chunk 46 optimal weight:    8.9990
   chunk 44 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   chunk 93 optimal weight:    5.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3849 r_free = 0.3849 target = 0.161616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.109420 restraints weight = 7802.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 1.66
r_work: 0.3044 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.1187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8400  Z= 0.158
  Angle     :  0.546   9.670  11369  Z= 0.298
  Chirality :  0.042   0.196   1280
  Planarity :  0.004   0.051   1448
  Dihedral  :  5.907  62.905   1164
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  :  9.37 %
    Favored  : 88.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.48 (0.26), residues: 1031
  helix:  2.49 (0.26), residues: 418
  sheet:  1.08 (0.34), residues: 214
  loop : -0.76 (0.29), residues: 399

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   0.006   0.000   ARG A  38 

*********************** 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: 21
    poor density    : 118
  time to evaluate  : 0.910 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8449 (tp40) cc_final: 0.8042 (tp-100)
REVERT: A  300 LYS cc_start: 0.6803 (OUTLIER) cc_final: 0.6334 (mtmt)
REVERT: A  314 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6679 (mt-10)
REVERT: B   70 TYR cc_start: 0.9135 (OUTLIER) cc_final: 0.7737 (m-80)
REVERT: C   29 LYS cc_start: 0.8235 (mmtm) cc_final: 0.7920 (mtpp)
REVERT: N    3 GLN cc_start: 0.8151 (tp40) cc_final: 0.7868 (tt0)
REVERT: R  115 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7438 (ttpp)
REVERT: R  261 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.5910 (mm-30)
  outliers start: 21
  outliers final: 9
  residues processed: 129
  average time/residue: 1.7024
  time to fit residues: 230.0435
Evaluate side-chains
  128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
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   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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 4 optimal weight:    9.9990
   chunk 16 optimal weight:    0.0770
   chunk 100 optimal weight:    8.9990
   chunk 2 optimal weight:    0.8980
   chunk 65 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 98 optimal weight:    8.9990
   chunk 82 optimal weight:    8.9990
   overall best weight:    1.9742

-------------------------------------------------------------------------------
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
R 197 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.159790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.109454 restraints weight = 7715.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 1.78
r_work: 0.3004 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2871 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.1258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8400  Z= 0.198
  Angle     :  0.594   9.483  11369  Z= 0.325
  Chirality :  0.044   0.195   1280
  Planarity :  0.004   0.052   1448
  Dihedral  :  5.993  59.779   1164
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  :  9.59 %
    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:  1.45 (0.26), residues: 1031
  helix:  2.49 (0.26), residues: 413
  sheet:  1.14 (0.34), residues: 211
  loop : -0.79 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 234 
 HIS   0.003   0.001   HIS B  65 
 PHE   0.015   0.002   PHE A 212 
 TYR   0.015   0.002   TYR A 339 
 ARG   0.006   0.000   ARG A  38 

*********************** 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: 22
    poor density    : 117
  time to evaluate  : 0.935 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8534 (tp40) cc_final: 0.8153 (tp-100)
REVERT: A  300 LYS cc_start: 0.6736 (OUTLIER) cc_final: 0.6259 (mtmt)
REVERT: A  314 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6694 (mt-10)
REVERT: B   70 TYR cc_start: 0.9159 (OUTLIER) cc_final: 0.8336 (m-80)
REVERT: C   29 LYS cc_start: 0.8375 (mmtm) cc_final: 0.8051 (mtpp)
REVERT: C   32 LYS cc_start: 0.7934 (tttm) cc_final: 0.7680 (mtpm)
REVERT: R  261 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.5939 (mm-30)
  outliers start: 22
  outliers final: 10
  residues processed: 128
  average time/residue: 1.6850
  time to fit residues: 225.5557
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  : 1.034 
-------------------------------------------------------------------------------
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   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:    4.9990
   chunk 50 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   chunk 73 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 59 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 6 optimal weight:    8.9990
   chunk 80 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   overall best weight:    3.5788

-------------------------------------------------------------------------------
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
R 197 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.158024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.110520 restraints weight = 7677.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 1.85
r_work: 0.2996 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2860 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.1430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8400  Z= 0.298
  Angle     :  0.698  10.597  11369  Z= 0.381
  Chirality :  0.048   0.194   1280
  Planarity :  0.005   0.053   1448
  Dihedral  :  6.247  56.116   1164
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  :  9.71 %
    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 (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:  1.14 (0.26), residues: 1031
  helix:  2.11 (0.25), residues: 413
  sheet:  1.16 (0.34), residues: 208
  loop : -0.91 (0.28), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP A 234 
 HIS   0.006   0.001   HIS B  65 
 PHE   0.017   0.002   PHE A 212 
 TYR   0.016   0.002   TYR A 339 
 ARG   0.006   0.001   ARG A  38 

*********************** 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
  141 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.961 
Fit side-chains
REVERT: A  300 LYS cc_start: 0.6757 (OUTLIER) cc_final: 0.6263 (mtmt)
REVERT: A  314 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6728 (mt-10)
REVERT: A  370 GLU cc_start: 0.5975 (mp0) cc_final: 0.5734 (tp30)
REVERT: B   70 TYR cc_start: 0.9149 (OUTLIER) cc_final: 0.8557 (m-80)
REVERT: B   96 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.6279 (m-10)
REVERT: R  261 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.5936 (mm-30)
  outliers start: 25
  outliers final: 12
  residues processed: 130
  average time/residue: 1.7370
  time to fit residues: 236.3631
Evaluate side-chains
  132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
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   96 TYR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain N residue   17 SER
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 88 optimal weight:    9.9990
   chunk 96 optimal weight:    7.9990
   chunk 17 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   chunk 80 optimal weight:    6.9990
   chunk 40 optimal weight:    4.9990
   chunk 55 optimal weight:    0.0770
   chunk 10 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   overall best weight:    1.9542

-------------------------------------------------------------------------------
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
R 197 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.159946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.107538 restraints weight = 7696.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 1.65
r_work: 0.3013 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2876 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8400  Z= 0.199
  Angle     :  0.598   9.035  11369  Z= 0.327
  Chirality :  0.044   0.196   1280
  Planarity :  0.004   0.053   1448
  Dihedral  :  5.984  54.403   1164
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  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:  1.35 (0.26), residues: 1031
  helix:  2.38 (0.26), residues: 413
  sheet:  1.16 (0.34), residues: 211
  loop : -0.87 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 234 
 HIS   0.003   0.001   HIS B 277 
 PHE   0.015   0.002   PHE A 212 
 TYR   0.015   0.002   TYR A 339 
 ARG   0.005   0.000   ARG A  38 

*********************** 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
  138 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.907 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8448 (tp40) cc_final: 0.8151 (tp-100)
REVERT: A  300 LYS cc_start: 0.6681 (OUTLIER) cc_final: 0.6206 (mtmt)
REVERT: A  314 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6668 (mt-10)
REVERT: B   70 TYR cc_start: 0.9152 (OUTLIER) cc_final: 0.8412 (m-80)
REVERT: R  261 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.5896 (mm-30)
  outliers start: 20
  outliers final: 10
  residues processed: 127
  average time/residue: 1.8104
  time to fit residues: 241.0249
Evaluate side-chains
  128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
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  246 ILE
Chi-restraints excluded: chain R residue  259 VAL
Chi-restraints excluded: chain R residue  261 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 82 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   chunk 94 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 100 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    1.7990

-------------------------------------------------------------------------------
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
R 197 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.160424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.108040 restraints weight = 7733.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 1.64
r_work: 0.3020 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2885 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.1300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8400  Z= 0.188
  Angle     :  0.584   8.929  11369  Z= 0.319
  Chirality :  0.044   0.196   1280
  Planarity :  0.004   0.053   1448
  Dihedral  :  5.895  52.517   1164
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 11.17 %
    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:  1.44 (0.26), residues: 1031
  helix:  2.50 (0.26), residues: 412
  sheet:  1.18 (0.34), residues: 211
  loop : -0.84 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 234 
 HIS   0.003   0.001   HIS B 277 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.015   0.002   TYR A 339 
 ARG   0.005   0.000   ARG A  38 

*********************** 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
  132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 1.014 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8399 (tp40) cc_final: 0.8168 (tp-100)
REVERT: A  300 LYS cc_start: 0.6704 (OUTLIER) cc_final: 0.6219 (mtmt)
REVERT: A  314 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6680 (mt-10)
REVERT: B   70 TYR cc_start: 0.9148 (OUTLIER) cc_final: 0.8344 (m-80)
REVERT: R  261 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.5897 (mm-30)
  outliers start: 19
  outliers final: 10
  residues processed: 122
  average time/residue: 1.8367
  time to fit residues: 234.2555
Evaluate side-chains
  125 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
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  246 ILE
Chi-restraints excluded: chain R residue  259 VAL
Chi-restraints excluded: chain R residue  261 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 92 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 77 optimal weight:    6.9990
   chunk 78 optimal weight:    5.9990
   chunk 63 optimal weight:    9.9990
   chunk 99 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   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
B 277 HIS
N   3 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 = 0.3848 r_free = 0.3848 target = 0.161531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.109121 restraints weight = 7821.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 1.66
r_work: 0.3039 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2905 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8400  Z= 0.166
  Angle     :  0.556   8.470  11369  Z= 0.303
  Chirality :  0.043   0.196   1280
  Planarity :  0.004   0.052   1448
  Dihedral  :  5.742  50.268   1164
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 11.74 %
    Favored  : 86.12 %
  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:  1.56 (0.26), residues: 1031
  helix:  2.65 (0.26), residues: 411
  sheet:  1.07 (0.34), residues: 217
  loop : -0.75 (0.29), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 234 
 HIS   0.004   0.001   HIS B 277 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.014   0.001   TYR A 339 
 ARG   0.005   0.000   ARG A  38 

*********************** 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: 19
    poor density    : 113
  time to evaluate  : 0.999 
Fit side-chains
REVERT: A  300 LYS cc_start: 0.6673 (OUTLIER) cc_final: 0.6189 (mtmt)
REVERT: A  314 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6670 (mt-10)
REVERT: B   70 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.8267 (m-80)
REVERT: C   29 LYS cc_start: 0.8240 (mmtm) cc_final: 0.7938 (mtpp)
REVERT: R  261 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.5933 (mm-30)
  outliers start: 19
  outliers final: 11
  residues processed: 122
  average time/residue: 1.7300
  time to fit residues: 220.9087
Evaluate side-chains
  121 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
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  246 ILE
Chi-restraints excluded: chain R residue  259 VAL
Chi-restraints excluded: chain R residue  261 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9990
   chunk 41 optimal weight:   10.0000
   chunk 50 optimal weight:    7.9990
   chunk 65 optimal weight:    1.9990
   chunk 63 optimal weight:    9.9990
   chunk 77 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  27 ASN
B 277 HIS
N   3 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 = 0.3857 r_free = 0.3857 target = 0.162314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.112880 restraints weight = 7705.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 1.90
r_work: 0.3037 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2904 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.1350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8400  Z= 0.154
  Angle     :  0.543   8.497  11369  Z= 0.295
  Chirality :  0.042   0.200   1280
  Planarity :  0.004   0.052   1448
  Dihedral  :  5.632  48.789   1164
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  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:  1.64 (0.26), residues: 1031
  helix:  2.74 (0.26), residues: 411
  sheet:  1.08 (0.34), residues: 217
  loop : -0.71 (0.29), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 234 
 HIS   0.004   0.001   HIS B 277 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.014   0.001   TYR A 339 
 ARG   0.005   0.000   ARG A  38 

********************** 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
  128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.916 
Fit side-chains
REVERT: A  300 LYS cc_start: 0.6666 (OUTLIER) cc_final: 0.6193 (mtmt)
REVERT: A  314 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6703 (mt-10)
REVERT: B   70 TYR cc_start: 0.9148 (OUTLIER) cc_final: 0.8269 (m-80)
REVERT: C   21 MET cc_start: 0.7556 (tpp) cc_final: 0.7003 (ttt)
REVERT: C   29 LYS cc_start: 0.8213 (mmtm) cc_final: 0.7926 (mtpp)
REVERT: R  115 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7439 (ttpp)
  outliers start: 14
  outliers final: 7
  residues processed: 121
  average time/residue: 1.6953
  time to fit residues: 214.9381
Evaluate side-chains
  121 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
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 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 10 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 94 optimal weight:    4.9990
   chunk 96 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
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
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 = 0.3834 r_free = 0.3834 target = 0.160360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.107697 restraints weight = 7822.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 1.66
r_work: 0.3018 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.1352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8400  Z= 0.202
  Angle     :  0.604   9.443  11369  Z= 0.327
  Chirality :  0.044   0.198   1280
  Planarity :  0.004   0.052   1448
  Dihedral  :  5.831  48.848   1164
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 12.19 %
    Favored  : 86.12 %
  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:  1.50 (0.26), residues: 1031
  helix:  2.55 (0.26), residues: 412
  sheet:  1.21 (0.34), residues: 211
  loop : -0.80 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 234 
 HIS   0.003   0.001   HIS B  65 
 PHE   0.015   0.002   PHE A 212 
 TYR   0.015   0.002   TYR A 339 
 ARG   0.005   0.000   ARG A  38 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8833.73 seconds
wall clock time: 155 minutes 42.52 seconds (9342.52 seconds total)