Starting phenix.real_space_refine
on Tue Mar  3 23:27:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7na7_24267/03_2026/7na7_24267.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7na7_24267/03_2026/7na7_24267.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7na7_24267/03_2026/7na7_24267.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7na7_24267/03_2026/7na7_24267.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7na7_24267/03_2026/7na7_24267.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7na7_24267/03_2026/7na7_24267.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      62      5.16       5
     C    5786      2.51       5
     N    1526      2.21       5
     O    1662      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9036
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1752
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1752
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2584
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
    Chain: "G"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 418
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
    Chain: "N"
      Number of atoms: 1784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1784
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2339
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2339
          Classifications: {'peptide': 291}
          Link IDs: {'PTRANS': 11, 'TRANS': 279}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 103
          Classifications: {'peptide': 12}
          Link IDs: {'PTRANS': 1, 'TRANS': 10}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'1IC:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'CLR': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.85, per 1000 atoms: 0.20
  Number of scatterers: 9036
  At special positions: 0
  Unit cell: (87.75, 120.25, 124.8, 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      62     16.00
     O    1662      8.00
     N    1526      7.00
     C    5786      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 159 " - pdb=" SG  CYS N 229 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 116 " - pdb=" SG  CYS R 198 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.76
  Conformation dependent library (CDL) restraints added in 401.5 milliseconds
  

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  1IC L   3 "
  Number of C-beta restraints generated:  2132

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 13 sheets defined
      38.0% alpha, 22.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 32
      removed outlier: 3.587A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.359A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.519A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.017A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.699A  pdb=" N   GLU A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.697A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 328 through 352
    Processing helix  chain 'B' and resid 7 through 22
      removed outlier: 3.545A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ASN B  16 " --> pdb=" O   GLU B  12 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 10 through 24
    Processing helix  chain 'G' and resid 30 through 44
      removed outlier: 4.444A  pdb=" N   ASP G  36 " --> pdb=" O   LYS G  32 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 40 through 71
      removed outlier: 4.142A  pdb=" N   ALA R  44 " --> pdb=" O   ALA R  40 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLY R  45 " --> pdb=" O   PRO R  41 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 72 through 75
    Processing helix  chain 'R' and resid 76 through 95
    Processing helix  chain 'R' and resid 95 through 105
    Processing helix  chain 'R' and resid 112 through 147
      removed outlier: 3.713A  pdb=" N   GLN R 120 " --> pdb=" O   CYS R 116 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   SER R 123 " --> pdb=" O   PHE R 119 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   TYR R 128 " --> pdb=" O   GLU R 124 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 147 through 155
      removed outlier: 3.607A  pdb=" N   VAL R 153 " --> pdb=" O   LEU R 149 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 157 through 176
      removed outlier: 3.570A  pdb=" N   LEU R 162 " --> pdb=" O   GLY R 158 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   VAL R 163 " --> pdb=" O   ARG R 159 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 177 through 182
    Processing helix  chain 'R' and resid 191 through 196
      removed outlier: 3.771A  pdb=" N   THR R 195 " --> pdb=" O   ASP R 191 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ASN R 196 " --> pdb=" O   PRO R 192 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 191 through 196'
    Processing helix  chain 'R' and resid 202 through 207
    Processing helix  chain 'R' and resid 208 through 243
      removed outlier: 3.512A  pdb=" N   SER R 218 " --> pdb=" O   VAL R 214 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ILE R 219 " --> pdb=" O   TRP R 215 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   PHE R 220 " --> pdb=" O   VAL R 216 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   PHE R 221 " --> pdb=" O   SER R 217 " (cutoff:3.500A)
      Proline residue:  R 224  - end of helix
      removed outlier: 3.509A  pdb=" N   ARG R 243 " --> pdb=" O   LEU R 239 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 256 through 290
      Proline residue:  R 278  - end of helix
      removed outlier: 3.757A  pdb=" N   PHE R 290 " --> pdb=" O   PHE R 286 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 295 through 325
      removed outlier: 4.074A  pdb=" N   GLN R 299 " --> pdb=" O   LEU R 295 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLN R 302 " --> pdb=" O   ALA R 298 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ALA R 316 " --> pdb=" O   PHE R 312 " (cutoff:3.500A)
      Proline residue:  R 320  - end of helix
    Processing helix  chain 'R' and resid 327 through 338
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.172A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.545A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.544A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.518A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.733A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.057A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.957A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.765A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.659A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.085A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.649A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.856A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.010A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (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: 6.802A  pdb=" N   MET N  34 " --> pdb=" O   TYR N  50 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   TYR N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12
      removed outlier: 4.223A  pdb=" N   PHE N 110 " --> pdb=" O   ARG N  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'N' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'N' and resid 146 through 148
      removed outlier: 6.345A  pdb=" N   LEU N 174 " --> pdb=" O   TYR N 190 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   TYR N 190 " --> pdb=" O   LEU N 174 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   TRP N 176 " --> pdb=" O   LEU N 188 " (cutoff:3.500A)

    442 hydrogen bonds defined for protein.
    1230 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.53

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1446
        1.30 -     1.43: 2481
        1.43 -     1.56: 5218
        1.56 -     1.69: 0
        1.69 -     1.82: 88
  Bond restraints: 9233
  Sorted by residual:
  bond pdb=" CA  SER N 106 "
       pdb=" CB  SER N 106 "
    ideal  model  delta    sigma   weight residual
    1.531  1.449  0.082 1.22e-02 6.72e+03 4.51e+01
  bond pdb=" C   PRO N 107 "
       pdb=" O   PRO N 107 "
    ideal  model  delta    sigma   weight residual
    1.234  1.169  0.064 1.14e-02 7.69e+03 3.17e+01
  bond pdb=" CA  SER N 105 "
       pdb=" CB  SER N 105 "
    ideal  model  delta    sigma   weight residual
    1.529  1.447  0.082 1.61e-02 3.86e+03 2.62e+01
  bond pdb=" C   LEU N 174 "
       pdb=" O   LEU N 174 "
    ideal  model  delta    sigma   weight residual
    1.236  1.177  0.058 1.14e-02 7.69e+03 2.62e+01
  bond pdb=" C   TYR N 175 "
       pdb=" O   TYR N 175 "
    ideal  model  delta    sigma   weight residual
    1.234  1.185  0.048 1.17e-02 7.31e+03 1.71e+01
  ... (remaining 9228 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.26: 12259
        3.26 -     6.51: 225
        6.51 -     9.77: 19
        9.77 -    13.03: 2
       13.03 -    16.28: 2
  Bond angle restraints: 12507
  Sorted by residual:
  angle pdb=" C   1IC L   3 "
        pdb=" CA  1IC L   3 "
        pdb=" CB  1IC L   3 "
      ideal   model   delta    sigma   weight residual
     110.50  126.38  -15.88 1.50e+00 4.44e-01 1.12e+02
  angle pdb=" C   GLN R 302 "
        pdb=" CA  GLN R 302 "
        pdb=" CB  GLN R 302 "
      ideal   model   delta    sigma   weight residual
     110.63  126.91  -16.28 1.85e+00 2.92e-01 7.75e+01
  angle pdb=" N   GLU A   8 "
        pdb=" CA  GLU A   8 "
        pdb=" C   GLU A   8 "
      ideal   model   delta    sigma   weight residual
     112.92  103.28    9.64 1.23e+00 6.61e-01 6.14e+01
  angle pdb=" C   ARG N 191 "
        pdb=" CA  ARG N 191 "
        pdb=" CB  ARG N 191 "
      ideal   model   delta    sigma   weight residual
     111.80  122.64  -10.84 1.46e+00 4.69e-01 5.51e+01
  angle pdb=" N   LEU R 103 "
        pdb=" CA  LEU R 103 "
        pdb=" C   LEU R 103 "
      ideal   model   delta    sigma   weight residual
     113.01  105.72    7.29 1.20e+00 6.94e-01 3.69e+01
  ... (remaining 12502 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.69: 5470
       34.69 -    69.38: 85
       69.38 -   104.07: 7
      104.07 -   138.76: 3
      138.76 -   173.45: 4
  Dihedral angle restraints: 5569
    sinusoidal: 2266
      harmonic: 3303
  Sorted by residual:
  dihedral pdb=" C   GLN R 302 "
           pdb=" N   GLN R 302 "
           pdb=" CA  GLN R 302 "
           pdb=" CB  GLN R 302 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -141.66   19.06     0      2.50e+00 1.60e-01 5.81e+01
  dihedral pdb=" C   ARG N 191 "
           pdb=" N   ARG N 191 "
           pdb=" CA  ARG N 191 "
           pdb=" CB  ARG N 191 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -140.00   17.40     0      2.50e+00 1.60e-01 4.84e+01
  dihedral pdb=" C   ASN R 305 "
           pdb=" N   ASN R 305 "
           pdb=" CA  ASN R 305 "
           pdb=" CB  ASN R 305 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.94   15.34     0      2.50e+00 1.60e-01 3.76e+01
  ... (remaining 5566 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.166: 1416
       1.166 -    2.333: 0
       2.333 -    3.499: 0
       3.499 -    4.665: 0
       4.665 -    5.831: 2
  Chirality restraints: 1418
  Sorted by residual:
  chirality pdb=" C13 CLR R 402 "
            pdb=" C12 CLR R 402 "
            pdb=" C14 CLR R 402 "
            pdb=" C17 CLR R 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93    2.90   -5.83 2.00e-01 2.50e+01 8.50e+02
  chirality pdb=" C17 CLR R 402 "
            pdb=" C13 CLR R 402 "
            pdb=" C16 CLR R 402 "
            pdb=" C20 CLR R 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55   -2.63    5.18 2.00e-01 2.50e+01 6.72e+02
  chirality pdb=" CA  1IC L   3 "
            pdb=" N   1IC L   3 "
            pdb=" C   1IC L   3 "
            pdb=" CB  1IC L   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.84   -0.65 2.00e-01 2.50e+01 1.04e+01
  ... (remaining 1415 not shown)

  Planarity restraints: 1566
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU N 174 "    0.026 2.00e-02 2.50e+03   5.27e-02 2.78e+01
        pdb=" C   LEU N 174 "   -0.091 2.00e-02 2.50e+03
        pdb=" O   LEU N 174 "    0.035 2.00e-02 2.50e+03
        pdb=" N   TYR N 175 "    0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A   6 "   -0.022 2.00e-02 2.50e+03   4.36e-02 1.90e+01
        pdb=" C   SER A   6 "    0.075 2.00e-02 2.50e+03
        pdb=" O   SER A   6 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   ALA A   7 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL N 147 "   -0.047 5.00e-02 4.00e+02   7.10e-02 8.06e+00
        pdb=" N   PRO N 148 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO N 148 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO N 148 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1563 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 566
        2.72 -     3.27: 8743
        3.27 -     3.81: 14984
        3.81 -     4.36: 19413
        4.36 -     4.90: 33264
  Nonbonded interactions: 76970
  Sorted by model distance:
  nonbonded pdb=" OG1 THR R  76 "
            pdb=" OD1 ASN R  79 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" O   GLY R  57 "
            pdb=" ND2 ASN R  61 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" O   MET G  38 "
            pdb=" OE1 GLU G  42 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   PRO R 192 "
            pdb=" OD1 ASN R 196 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   PHE N  32 "
            pdb=" NH2 ARG N  72 "
     model   vdw
     2.322 3.120
  ... (remaining 76965 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:             6.360
  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:          0.290
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     9.570
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:7.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7195
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      :  0.006   0.082   9236  Z= 0.382
  Angle     :  1.043  16.282  12513  Z= 0.655
  Chirality :  0.218   5.831   1418
  Planarity :  0.006   0.071   1566
  Dihedral  : 14.699 173.449   3428
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  3.98 %
    Favored  : 95.41 %
  Cbeta Deviations :  0.47 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.23), residues: 1119
  helix:  0.86 (0.26), residues: 388
  sheet:  0.67 (0.28), residues: 298
  loop : -0.62 (0.26), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 214 
 TYR   0.034   0.003   TYR N 102 
 PHE   0.019   0.002   PHE R 179 
 TRP   0.017   0.002   TRP N 176 
 HIS   0.008   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00620 ( 9233)
  covalent geometry    : angle       1.04259 (12507)
  SS BOND              : bond        0.00460 (    3)
  SS BOND              : angle       1.09701 (    6)
  hydrogen bonds       : bond        0.17976 (  437)
  hydrogen bonds       : angle       6.76181 ( 1230)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 237
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.7165 (m-30) cc_final: 0.6770 (m-30)
REVERT: A  186 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6501 (mt-10)
REVERT: A  245 GLU cc_start: 0.6504 (tp30) cc_final: 0.6069 (tp30)
REVERT: A  316 THR cc_start: 0.8443 (m) cc_final: 0.8046 (p)
REVERT: B  137 ARG cc_start: 0.7770 (tpp-160) cc_final: 0.7519 (tpt90)
REVERT: N  150 THR cc_start: 0.8011 (t) cc_final: 0.7784 (p)
REVERT: R  237 ARG cc_start: 0.7084 (ttp80) cc_final: 0.6751 (ttp80)
REVERT: R  283 ARG cc_start: 0.6910 (mtp85) cc_final: 0.6671 (mtt-85)
REVERT: R  327 SER cc_start: 0.7871 (t) cc_final: 0.7481 (p)
REVERT: L   10 GLN cc_start: 0.5134 (mt0) cc_final: 0.4931 (pm20)
  outliers start: 6
  outliers final: 0
  residues processed: 241
  average time/residue: 0.5116
  time to fit residues: 131.9953
Evaluate side-chains
  205 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.4980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    0.5980
   chunk 106 optimal weight:    2.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  16 ASN
B 230 ASN
B 295 ASN
N  82 GLN
N 142 GLN
N 179 GLN
N 183 GLN
R 120 GLN
R 302 GLN
R 319 ASN
L   9 HIS
L  10 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.123713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.111372 restraints weight = 12825.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.49
r_work: 0.3371 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.2305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9236  Z= 0.164
  Angle     :  0.788  30.909  12513  Z= 0.367
  Chirality :  0.063   1.705   1418
  Planarity :  0.005   0.053   1566
  Dihedral  : 12.079 179.717   1375
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 13.35 %
    Favored  : 84.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.24), residues: 1119
  helix:  1.23 (0.26), residues: 396
  sheet:  0.75 (0.28), residues: 295
  loop : -0.48 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 208 
 TYR   0.022   0.002   TYR N 190 
 PHE   0.024   0.002   PHE A 189 
 TRP   0.018   0.002   TRP B 169 
 HIS   0.008   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 9233)
  covalent geometry    : angle       0.78756 (12507)
  SS BOND              : bond        0.00195 (    3)
  SS BOND              : angle       0.90238 (    6)
  hydrogen bonds       : bond        0.04675 (  437)
  hydrogen bonds       : angle       4.90958 ( 1230)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 219
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.7914 (m-30) cc_final: 0.7601 (m-30)
REVERT: A   29 LYS cc_start: 0.8257 (tttm) cc_final: 0.8030 (tttm)
REVERT: A  243 MET cc_start: 0.8641 (tpp) cc_final: 0.8374 (tpp)
REVERT: A  245 GLU cc_start: 0.7410 (tp30) cc_final: 0.7064 (tp30)
REVERT: A  324 THR cc_start: 0.7538 (m) cc_final: 0.6864 (p)
REVERT: A  341 ASP cc_start: 0.8104 (t0) cc_final: 0.7904 (t0)
REVERT: A  345 LYS cc_start: 0.8542 (mttt) cc_final: 0.8275 (mttt)
REVERT: B  111 TYR cc_start: 0.8473 (m-80) cc_final: 0.8268 (m-80)
REVERT: R  142 TYR cc_start: 0.8564 (t80) cc_final: 0.8323 (t80)
REVERT: R  150 ARG cc_start: 0.8181 (ttm110) cc_final: 0.7970 (ttm170)
REVERT: R  237 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7605 (ttp80)
REVERT: L   10 GLN cc_start: 0.6096 (mt0) cc_final: 0.5528 (pm20)
  outliers start: 25
  outliers final: 11
  residues processed: 228
  average time/residue: 0.5440
  time to fit residues: 132.2269
Evaluate side-chains
  213 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 202
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue  158 SER
Chi-restraints excluded: chain N residue  184 SER
Chi-restraints excluded: chain R residue   73 GLU
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  307 VAL
Chi-restraints excluded: chain R residue  328 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9980
   chunk 82 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 98 optimal weight:    0.0270
   chunk 101 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
B 295 ASN
G  17 GLN
N 179 GLN
** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   9 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.121230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.109109 restraints weight = 12735.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 1.47
r_work: 0.3337 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.3009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9236  Z= 0.178
  Angle     :  0.762  31.548  12513  Z= 0.350
  Chirality :  0.063   1.715   1418
  Planarity :  0.004   0.054   1566
  Dihedral  : 11.791 176.858   1375
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 14.17 %
    Favored  : 82.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.24), residues: 1119
  helix:  1.28 (0.26), residues: 389
  sheet:  0.67 (0.29), residues: 296
  loop : -0.51 (0.28), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 283 
 TYR   0.015   0.002   TYR N 190 
 PHE   0.018   0.002   PHE A 189 
 TRP   0.018   0.002   TRP B 169 
 HIS   0.006   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 9233)
  covalent geometry    : angle       0.76153 (12507)
  SS BOND              : bond        0.00341 (    3)
  SS BOND              : angle       0.92579 (    6)
  hydrogen bonds       : bond        0.04747 (  437)
  hydrogen bonds       : angle       4.72807 ( 1230)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 216
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.7913 (m-30) cc_final: 0.7614 (m-30)
REVERT: A  245 GLU cc_start: 0.7360 (tp30) cc_final: 0.7054 (tp30)
REVERT: A  324 THR cc_start: 0.7624 (m) cc_final: 0.6914 (p)
REVERT: A  341 ASP cc_start: 0.8008 (t0) cc_final: 0.7757 (t0)
REVERT: B  155 ASN cc_start: 0.8314 (t0) cc_final: 0.8101 (t0)
REVERT: N  202 ARG cc_start: 0.8178 (ttp-110) cc_final: 0.7925 (ttm170)
REVERT: R  142 TYR cc_start: 0.8550 (t80) cc_final: 0.8289 (t80)
REVERT: R  150 ARG cc_start: 0.8154 (ttm110) cc_final: 0.7919 (ttm170)
REVERT: R  237 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7603 (ttp80)
REVERT: R  283 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7292 (mtt180)
REVERT: R  332 VAL cc_start: 0.8570 (p) cc_final: 0.8253 (m)
  outliers start: 37
  outliers final: 17
  residues processed: 233
  average time/residue: 0.5026
  time to fit residues: 125.5702
Evaluate side-chains
  217 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 199
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  184 SER
Chi-restraints excluded: chain R residue   69 SER
Chi-restraints excluded: chain R residue   88 SER
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  283 ARG
Chi-restraints excluded: chain R residue  307 VAL
Chi-restraints excluded: chain R residue  328 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 57 optimal weight:    0.2980
   chunk 65 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 50 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN
B 295 ASN
N  82 GLN
N 179 GLN
R 302 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.121645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.109474 restraints weight = 12945.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.48
r_work: 0.3351 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.3284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9236  Z= 0.165
  Angle     :  0.754  31.829  12513  Z= 0.341
  Chirality :  0.063   1.717   1418
  Planarity :  0.004   0.056   1566
  Dihedral  : 11.940 178.106   1375
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 15.80 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.24), residues: 1119
  helix:  1.34 (0.26), residues: 390
  sheet:  0.59 (0.28), residues: 296
  loop : -0.49 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  32 
 TYR   0.013   0.001   TYR N 190 
 PHE   0.016   0.001   PHE A 189 
 TRP   0.018   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 9233)
  covalent geometry    : angle       0.75383 (12507)
  SS BOND              : bond        0.00243 (    3)
  SS BOND              : angle       1.50879 (    6)
  hydrogen bonds       : bond        0.04418 (  437)
  hydrogen bonds       : angle       4.67791 ( 1230)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 200
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.7947 (m-30) cc_final: 0.7643 (m-30)
REVERT: A  245 GLU cc_start: 0.7389 (tp30) cc_final: 0.7101 (tp30)
REVERT: B   52 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8268 (mtt-85)
REVERT: B  155 ASN cc_start: 0.8353 (t0) cc_final: 0.8093 (t0)
REVERT: B  249 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8217 (m)
REVERT: R  142 TYR cc_start: 0.8550 (t80) cc_final: 0.8318 (t80)
REVERT: R  150 ARG cc_start: 0.8170 (ttm110) cc_final: 0.7937 (ttm170)
REVERT: R  237 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7591 (ttp80)
REVERT: R  283 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7258 (mtt180)
REVERT: R  332 VAL cc_start: 0.8564 (p) cc_final: 0.8263 (m)
  outliers start: 34
  outliers final: 21
  residues processed: 218
  average time/residue: 0.5354
  time to fit residues: 124.6095
Evaluate side-chains
  220 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 196
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  184 SER
Chi-restraints excluded: chain N residue  219 LEU
Chi-restraints excluded: chain R residue   69 SER
Chi-restraints excluded: chain R residue   88 SER
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  283 ARG
Chi-restraints excluded: chain R residue  300 ILE
Chi-restraints excluded: chain R residue  307 VAL
Chi-restraints excluded: chain R residue  328 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 63 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 92 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9990
   chunk 79 optimal weight:    0.0870
   chunk 72 optimal weight:    0.0010
   chunk 27 optimal weight:    0.7980
   chunk 98 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.4764

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN
B  44 GLN
B 220 GLN
B 239 ASN
B 295 ASN
N  82 GLN
N 179 GLN
R 186 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.123581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.111091 restraints weight = 12414.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.50
r_work: 0.3367 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.3503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9236  Z= 0.141
  Angle     :  0.736  30.736  12513  Z= 0.330
  Chirality :  0.063   1.739   1418
  Planarity :  0.004   0.056   1566
  Dihedral  : 11.778 172.652   1375
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 17.33 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.68 (0.24), residues: 1119
  helix:  1.51 (0.26), residues: 388
  sheet:  0.45 (0.29), residues: 285
  loop : -0.41 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B  42 
 TYR   0.013   0.001   TYR N 190 
 PHE   0.017   0.001   PHE A 189 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 9233)
  covalent geometry    : angle       0.73574 (12507)
  SS BOND              : bond        0.00233 (    3)
  SS BOND              : angle       1.47202 (    6)
  hydrogen bonds       : bond        0.04162 (  437)
  hydrogen bonds       : angle       4.55881 ( 1230)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 201
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.8002 (m-30) cc_final: 0.7669 (m-30)
REVERT: A  243 MET cc_start: 0.8483 (tpp) cc_final: 0.8261 (tpp)
REVERT: A  245 GLU cc_start: 0.7374 (tp30) cc_final: 0.7077 (tp30)
REVERT: B  150 ARG cc_start: 0.8847 (mmt-90) cc_final: 0.8618 (mpt180)
REVERT: N  202 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8089 (ttp-170)
REVERT: R   82 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8022 (mm)
REVERT: R  124 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7310 (mm-30)
REVERT: R  142 TYR cc_start: 0.8551 (t80) cc_final: 0.8335 (t80)
REVERT: R  150 ARG cc_start: 0.8115 (ttm110) cc_final: 0.7875 (ttm170)
REVERT: R  237 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7631 (ttp80)
REVERT: R  283 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7106 (mtt180)
REVERT: R  332 VAL cc_start: 0.8539 (p) cc_final: 0.8244 (m)
  outliers start: 28
  outliers final: 17
  residues processed: 217
  average time/residue: 0.5271
  time to fit residues: 122.2326
Evaluate side-chains
  219 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 199
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  202 ARG
Chi-restraints excluded: chain N residue  219 LEU
Chi-restraints excluded: chain R residue   69 SER
Chi-restraints excluded: chain R residue   82 LEU
Chi-restraints excluded: chain R residue   88 SER
Chi-restraints excluded: chain R residue   99 ASP
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  283 ARG
Chi-restraints excluded: chain R residue  300 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 66 optimal weight:    0.4980
   chunk 67 optimal weight:    0.9980
   chunk 100 optimal weight:    0.5980
   chunk 94 optimal weight:    2.9990
   chunk 96 optimal weight:    0.1980
   chunk 8 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  44 GLN
B 239 ASN
B 295 ASN
N 142 GLN
N 179 GLN
R 186 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.123423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.110921 restraints weight = 12350.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 1.51
r_work: 0.3362 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.3690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9236  Z= 0.150
  Angle     :  0.736  30.798  12513  Z= 0.331
  Chirality :  0.063   1.764   1418
  Planarity :  0.004   0.059   1566
  Dihedral  : 11.610 172.998   1375
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 17.02 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.68 (0.25), residues: 1119
  helix:  1.51 (0.27), residues: 388
  sheet:  0.41 (0.29), residues: 285
  loop : -0.38 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  32 
 TYR   0.012   0.001   TYR R 313 
 PHE   0.015   0.001   PHE A 189 
 TRP   0.017   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 9233)
  covalent geometry    : angle       0.73531 (12507)
  SS BOND              : bond        0.00300 (    3)
  SS BOND              : angle       1.58568 (    6)
  hydrogen bonds       : bond        0.04155 (  437)
  hydrogen bonds       : angle       4.54852 ( 1230)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 207
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.8017 (m-30) cc_final: 0.7688 (m-30)
REVERT: A  243 MET cc_start: 0.8489 (tpp) cc_final: 0.8263 (tpp)
REVERT: A  245 GLU cc_start: 0.7341 (tp30) cc_final: 0.7057 (tp30)
REVERT: B   42 ARG cc_start: 0.7399 (mmm-85) cc_final: 0.7137 (mmm-85)
REVERT: N  140 MET cc_start: 0.8440 (mmm) cc_final: 0.8240 (mmt)
REVERT: N  202 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8024 (ttp-170)
REVERT: R   82 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8037 (mm)
REVERT: R  124 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7359 (mm-30)
REVERT: R  142 TYR cc_start: 0.8542 (t80) cc_final: 0.8342 (t80)
REVERT: R  150 ARG cc_start: 0.8086 (ttm110) cc_final: 0.7834 (ttm170)
REVERT: R  237 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7644 (ttp80)
REVERT: R  283 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7126 (mtt180)
REVERT: R  332 VAL cc_start: 0.8532 (p) cc_final: 0.8235 (m)
  outliers start: 33
  outliers final: 20
  residues processed: 221
  average time/residue: 0.5630
  time to fit residues: 132.6907
Evaluate side-chains
  226 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 203
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   23 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  184 SER
Chi-restraints excluded: chain N residue  202 ARG
Chi-restraints excluded: chain N residue  219 LEU
Chi-restraints excluded: chain R residue   69 SER
Chi-restraints excluded: chain R residue   82 LEU
Chi-restraints excluded: chain R residue   88 SER
Chi-restraints excluded: chain R residue   99 ASP
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  283 ARG
Chi-restraints excluded: chain R residue  300 ILE
Chi-restraints excluded: chain R residue  328 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0670
   chunk 92 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 91 optimal weight:    0.4980
   chunk 85 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN
B 156 GLN
B 239 ASN
N  82 GLN
N 142 GLN
N 179 GLN
R 186 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.123421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.110869 restraints weight = 12422.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 1.51
r_work: 0.3365 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.3756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9236  Z= 0.154
  Angle     :  0.742  30.597  12513  Z= 0.333
  Chirality :  0.064   1.782   1418
  Planarity :  0.004   0.061   1566
  Dihedral  : 11.598 173.362   1375
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 18.25 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.25), residues: 1119
  helix:  1.56 (0.27), residues: 381
  sheet:  0.39 (0.29), residues: 291
  loop : -0.36 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  32 
 TYR   0.012   0.001   TYR R 313 
 PHE   0.016   0.001   PHE A 189 
 TRP   0.018   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 9233)
  covalent geometry    : angle       0.74120 (12507)
  SS BOND              : bond        0.00273 (    3)
  SS BOND              : angle       1.52766 (    6)
  hydrogen bonds       : bond        0.04182 (  437)
  hydrogen bonds       : angle       4.53918 ( 1230)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 205
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.8005 (m-30) cc_final: 0.7656 (m-30)
REVERT: A  243 MET cc_start: 0.8468 (tpp) cc_final: 0.8227 (tpp)
REVERT: A  245 GLU cc_start: 0.7338 (tp30) cc_final: 0.7048 (tp30)
REVERT: A  260 THR cc_start: 0.8671 (m) cc_final: 0.8402 (p)
REVERT: B   42 ARG cc_start: 0.7430 (mmm-85) cc_final: 0.7123 (mmm-85)
REVERT: B  219 ARG cc_start: 0.8219 (mtt-85) cc_final: 0.7981 (mmt-90)
REVERT: B  258 ASP cc_start: 0.7893 (t0) cc_final: 0.7625 (t0)
REVERT: N  140 MET cc_start: 0.8469 (mmm) cc_final: 0.8255 (mmt)
REVERT: N  202 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8057 (ttp-170)
REVERT: R   82 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8006 (mm)
REVERT: R  142 TYR cc_start: 0.8534 (t80) cc_final: 0.8306 (t80)
REVERT: R  150 ARG cc_start: 0.8079 (ttm110) cc_final: 0.7820 (ttm170)
REVERT: R  237 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7644 (ttp80)
REVERT: R  270 PHE cc_start: 0.7602 (m-10) cc_final: 0.7367 (m-80)
REVERT: R  283 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7295 (mtt180)
  outliers start: 28
  outliers final: 18
  residues processed: 218
  average time/residue: 0.5367
  time to fit residues: 124.8618
Evaluate side-chains
  226 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 205
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  184 SER
Chi-restraints excluded: chain N residue  202 ARG
Chi-restraints excluded: chain N residue  219 LEU
Chi-restraints excluded: chain R residue   82 LEU
Chi-restraints excluded: chain R residue   88 SER
Chi-restraints excluded: chain R residue   99 ASP
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  283 ARG
Chi-restraints excluded: chain R residue  300 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 104 optimal weight:    0.7980
   chunk 88 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 239 ASN
N  82 GLN
N 142 GLN
N 179 GLN
R 186 HIS
L   9 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.121839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.109424 restraints weight = 12348.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 1.50
r_work: 0.3345 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.3879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9236  Z= 0.214
  Angle     :  0.781  30.522  12513  Z= 0.356
  Chirality :  0.066   1.788   1418
  Planarity :  0.004   0.065   1566
  Dihedral  : 11.690 173.683   1375
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 18.14 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.25), residues: 1119
  helix:  1.32 (0.27), residues: 381
  sheet:  0.40 (0.29), residues: 301
  loop : -0.43 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A  32 
 TYR   0.014   0.002   TYR R 313 
 PHE   0.018   0.002   PHE A 189 
 TRP   0.019   0.002   TRP B 169 
 HIS   0.005   0.001   HIS L   9 

Details of bonding type rmsd
  covalent geometry    : bond        0.00516 ( 9233)
  covalent geometry    : angle       0.78044 (12507)
  SS BOND              : bond        0.00368 (    3)
  SS BOND              : angle       1.87737 (    6)
  hydrogen bonds       : bond        0.04530 (  437)
  hydrogen bonds       : angle       4.71474 ( 1230)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 201
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.8007 (m-30) cc_final: 0.7667 (m-30)
REVERT: A  197 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.8055 (mttm)
REVERT: A  243 MET cc_start: 0.8455 (tpp) cc_final: 0.8213 (tpp)
REVERT: A  245 GLU cc_start: 0.7315 (tp30) cc_final: 0.7039 (tp30)
REVERT: A  260 THR cc_start: 0.8691 (m) cc_final: 0.8408 (p)
REVERT: A  324 THR cc_start: 0.7644 (m) cc_final: 0.7079 (p)
REVERT: B   42 ARG cc_start: 0.7462 (mmm-85) cc_final: 0.7140 (mmm-85)
REVERT: B  258 ASP cc_start: 0.7867 (t0) cc_final: 0.7459 (t0)
REVERT: N  140 MET cc_start: 0.8515 (mmm) cc_final: 0.8271 (mmt)
REVERT: N  202 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8074 (ttp-170)
REVERT: R  142 TYR cc_start: 0.8536 (t80) cc_final: 0.8311 (t80)
REVERT: R  237 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7665 (ttp80)
REVERT: R  283 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7354 (mtt180)
  outliers start: 40
  outliers final: 21
  residues processed: 219
  average time/residue: 0.5216
  time to fit residues: 122.0945
Evaluate side-chains
  225 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 201
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   23 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue  184 SER
Chi-restraints excluded: chain N residue  202 ARG
Chi-restraints excluded: chain N residue  219 LEU
Chi-restraints excluded: chain R residue   88 SER
Chi-restraints excluded: chain R residue   99 ASP
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  283 ARG
Chi-restraints excluded: chain R residue  307 VAL
Chi-restraints excluded: chain R residue  328 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 107 optimal weight:    0.8980
   chunk 108 optimal weight:    0.5980
   chunk 97 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0770
   chunk 44 optimal weight:    0.5980
   chunk 78 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 156 GLN
B 239 ASN
B 293 ASN
N 142 GLN
N 179 GLN
R 186 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.123149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.110592 restraints weight = 12297.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 1.50
r_work: 0.3362 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.3961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9236  Z= 0.151
  Angle     :  0.755  30.429  12513  Z= 0.339
  Chirality :  0.064   1.794   1418
  Planarity :  0.004   0.064   1566
  Dihedral  : 11.605 174.058   1375
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 19.47 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.25), residues: 1119
  helix:  1.47 (0.27), residues: 380
  sheet:  0.26 (0.29), residues: 291
  loop : -0.37 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A  32 
 TYR   0.012   0.001   TYR R 313 
 PHE   0.016   0.001   PHE A 189 
 TRP   0.019   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 9233)
  covalent geometry    : angle       0.75487 (12507)
  SS BOND              : bond        0.00257 (    3)
  SS BOND              : angle       1.41800 (    6)
  hydrogen bonds       : bond        0.04184 (  437)
  hydrogen bonds       : angle       4.61606 ( 1230)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 197
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.8020 (m-30) cc_final: 0.7669 (m-30)
REVERT: A  197 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.8055 (mttm)
REVERT: A  243 MET cc_start: 0.8425 (tpp) cc_final: 0.8185 (tpp)
REVERT: A  245 GLU cc_start: 0.7291 (tp30) cc_final: 0.7020 (tp30)
REVERT: A  260 THR cc_start: 0.8678 (m) cc_final: 0.8387 (p)
REVERT: A  324 THR cc_start: 0.7563 (m) cc_final: 0.6996 (p)
REVERT: B   42 ARG cc_start: 0.7445 (mmm-85) cc_final: 0.7127 (mmm-85)
REVERT: B  304 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.6661 (tmm-80)
REVERT: N  140 MET cc_start: 0.8491 (mmm) cc_final: 0.8254 (mmt)
REVERT: N  202 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8056 (ttp-170)
REVERT: R  142 TYR cc_start: 0.8522 (t80) cc_final: 0.8314 (t80)
REVERT: R  237 ARG cc_start: 0.7988 (ttp80) cc_final: 0.7668 (ttp80)
REVERT: R  283 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7326 (mtt180)
  outliers start: 32
  outliers final: 21
  residues processed: 210
  average time/residue: 0.5389
  time to fit residues: 120.9711
Evaluate side-chains
  222 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 197
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   23 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue  184 SER
Chi-restraints excluded: chain N residue  202 ARG
Chi-restraints excluded: chain N residue  219 LEU
Chi-restraints excluded: chain R residue   88 SER
Chi-restraints excluded: chain R residue   99 ASP
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  283 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 106 optimal weight:    0.0980
   chunk 93 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 94 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0570
   chunk 102 optimal weight:    0.8980
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 156 GLN
B 239 ASN
B 293 ASN
N 142 GLN
N 179 GLN
R 186 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.123437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.110900 restraints weight = 12264.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.50
r_work: 0.3367 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.4002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9236  Z= 0.149
  Angle     :  0.750  30.436  12513  Z= 0.337
  Chirality :  0.064   1.792   1418
  Planarity :  0.004   0.065   1566
  Dihedral  : 11.571 174.417   1375
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 19.47 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.25), residues: 1119
  helix:  1.51 (0.27), residues: 382
  sheet:  0.23 (0.29), residues: 286
  loop : -0.38 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A  32 
 TYR   0.011   0.001   TYR R 313 
 PHE   0.015   0.001   PHE A 189 
 TRP   0.018   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 9233)
  covalent geometry    : angle       0.74923 (12507)
  SS BOND              : bond        0.00247 (    3)
  SS BOND              : angle       1.44131 (    6)
  hydrogen bonds       : bond        0.04123 (  437)
  hydrogen bonds       : angle       4.59264 ( 1230)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 198
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.7978 (m-30) cc_final: 0.7626 (m-30)
REVERT: A  197 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.8051 (mttm)
REVERT: A  243 MET cc_start: 0.8432 (tpp) cc_final: 0.8148 (tpp)
REVERT: A  245 GLU cc_start: 0.7287 (tp30) cc_final: 0.7026 (tp30)
REVERT: A  260 THR cc_start: 0.8679 (m) cc_final: 0.8383 (p)
REVERT: A  324 THR cc_start: 0.7567 (m) cc_final: 0.6989 (p)
REVERT: B  215 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6537 (pp20)
REVERT: N  140 MET cc_start: 0.8481 (mmm) cc_final: 0.8238 (mmt)
REVERT: N  202 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8056 (ttp-170)
REVERT: R  142 TYR cc_start: 0.8524 (t80) cc_final: 0.8316 (t80)
REVERT: R  150 ARG cc_start: 0.8068 (ttm110) cc_final: 0.7805 (ttm170)
REVERT: R  237 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7675 (ttp80)
REVERT: R  283 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7327 (mtt180)
  outliers start: 29
  outliers final: 22
  residues processed: 210
  average time/residue: 0.5595
  time to fit residues: 125.3498
Evaluate side-chains
  227 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 201
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   23 SER
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue  184 SER
Chi-restraints excluded: chain N residue  202 ARG
Chi-restraints excluded: chain N residue  219 LEU
Chi-restraints excluded: chain R residue   88 SER
Chi-restraints excluded: chain R residue   99 ASP
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  283 ARG
Chi-restraints excluded: chain R residue  328 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0670
   chunk 75 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 58 optimal weight:    0.4980
   chunk 15 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 105 optimal weight:    0.0970
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.4116

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 156 GLN
B 239 ASN
B 293 ASN
N 142 GLN
N 179 GLN
R 186 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.123944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.111459 restraints weight = 12209.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 1.50
r_work: 0.3375 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3241 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.4043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9236  Z= 0.132
  Angle     :  0.738  30.423  12513  Z= 0.330
  Chirality :  0.063   1.791   1418
  Planarity :  0.004   0.064   1566
  Dihedral  : 11.520 174.710   1375
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 19.37 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.25), residues: 1119
  helix:  1.61 (0.27), residues: 382
  sheet:  0.28 (0.29), residues: 288
  loop : -0.39 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A  32 
 TYR   0.011   0.001   TYR N 190 
 PHE   0.016   0.001   PHE R 309 
 TRP   0.018   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 9233)
  covalent geometry    : angle       0.73731 (12507)
  SS BOND              : bond        0.00198 (    3)
  SS BOND              : angle       1.32718 (    6)
  hydrogen bonds       : bond        0.03974 (  437)
  hydrogen bonds       : angle       4.51617 ( 1230)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3779.71 seconds
wall clock time: 65 minutes 4.03 seconds (3904.03 seconds total)