Starting phenix.real_space_refine
on Thu Jul  2 16:09:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/20zc_67426/07_2026/20zc_67426.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/20zc_67426/07_2026/20zc_67426.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/20zc_67426/07_2026/20zc_67426.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/20zc_67426/07_2026/20zc_67426.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/20zc_67426/07_2026/20zc_67426.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/20zc_67426/07_2026/20zc_67426.cif"
  }
  resolution = 2.6
  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=   0.013
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      61      5.16       5
     C    5684      2.51       5
     N    1521      2.21       5
     O    1666      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8932
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1747
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1747
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 2584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2584
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "C"
      Number of atoms: 404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 404
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "D"
      Number of atoms: 1762
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1762
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 12
    Chain: "L"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 53
          Classifications: {'peptide': 6}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 4}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "R"
      Number of atoms: 2382
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2382
          Classifications: {'peptide': 306}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 9, 'TRANS': 296}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 53
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 42
  Time building chain proxies: 1.84, per 1000 atoms: 0.21
  Number of scatterers: 8932
  At special positions: 0
  Unit cell: (92.127, 125.706, 136.038, 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      61     16.00
     O    1666      8.00
     N    1521      7.00
     C    5684      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 147 " - pdb=" SG  CYS D 217 " distance=2.72
    Simple disulfide: pdb=" SG  CYS R 141 " - pdb=" SG  CYS R 224 " distance=2.85

  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: 0.50
  Conformation dependent library (CDL) restraints added in 421.7 milliseconds
  

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2160

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 14 sheets defined
      39.3% alpha, 23.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.518A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.983A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.838A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.337A  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 281
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 327 through 352
      removed outlier: 3.719A  pdb=" N   ASN A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   VAL A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   PHE A 334 " --> pdb=" O   LYS A 330 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   PHE A 336 " --> pdb=" O   VAL A 332 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   LYS A 349 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ASP A 350 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 3.627A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.702A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 24
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.501A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 28 through 32
    Processing helix  chain 'D' and resid 62 through 65
    Processing helix  chain 'D' and resid 87 through 91
    Processing helix  chain 'R' and resid 51 through 55
    Processing helix  chain 'R' and resid 59 through 91
    Processing helix  chain 'R' and resid 97 through 128
      removed outlier: 3.778A  pdb=" N   HIS R 104 " --> pdb=" O   THR R 100 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   LEU R 108 " --> pdb=" O   HIS R 104 " (cutoff:3.500A)
      Proline residue:  R 121  - end of helix
      removed outlier: 3.571A  pdb=" N   TYR R 125 " --> pdb=" O   PRO R 121 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 136 through 172
      removed outlier: 3.739A  pdb=" N   GLY R 140 " --> pdb=" O   PHE R 136 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 172 through 180
    Processing helix  chain 'R' and resid 181 through 199
      removed outlier: 3.546A  pdb=" N   THR R 185 " --> pdb=" O   SER R 181 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 201 through 206
      removed outlier: 4.150A  pdb=" N   PHE R 205 " --> pdb=" O   VAL R 201 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   THR R 206 " --> pdb=" O   PRO R 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 201 through 206'
    Processing helix  chain 'R' and resid 229 through 245
      removed outlier: 3.684A  pdb=" N   VAL R 235 " --> pdb=" O   ALA R 231 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 245 through 273
      removed outlier: 3.506A  pdb=" N   VAL R 251 " --> pdb=" O   PHE R 247 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ALA R 271 " --> pdb=" O   VAL R 267 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 295 through 329
      removed outlier: 3.719A  pdb=" N   ARG R 306 " --> pdb=" O   VAL R 302 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   VAL R 309 " --> pdb=" O   LEU R 305 " (cutoff:3.500A)
      Proline residue:  R 318  - end of helix
    Processing helix  chain 'R' and resid 335 through 365
      removed outlier: 3.624A  pdb=" N   SER R 357 " --> pdb=" O   PHE R 353 " (cutoff:3.500A)
      Proline residue:  R 361  - end of helix
    Processing helix  chain 'R' and resid 369 through 375
      removed outlier: 3.620A  pdb=" N   HIS R 373 " --> pdb=" O   ALA R 369 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.319A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 9.284A  pdb=" N   ALA A 220 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.200A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.972A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 9.304A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.888A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 8.057A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.556A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.839A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.787A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.898A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.693A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA B 167 " --> pdb=" O   THR B 159 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.042A  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: 6.825A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.341A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.523A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.942A  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: 3.861A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12
      removed outlier: 3.505A  pdb=" N   THR D 118 " --> pdb=" O   GLY D  10 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   MET D  34 " --> pdb=" O   TYR D  50 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   TYR D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   TYR D  59 " --> pdb=" O   TYR D  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12
      removed outlier: 3.505A  pdb=" N   THR D 118 " --> pdb=" O   GLY D  10 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   PHE D 110 " --> pdb=" O   ARG D  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 130
    Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 136
      removed outlier: 6.142A  pdb=" N   LEU D 162 " --> pdb=" O   TYR D 178 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   TYR D 178 " --> pdb=" O   LEU D 162 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   TRP D 164 " --> pdb=" O   LEU D 176 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 207 through 211
      removed outlier: 3.532A  pdb=" N   THR R 225 " --> pdb=" O   GLY R 208 " (cutoff:3.500A)

    462 hydrogen bonds defined for protein.
    1287 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: 1.39

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1449
        1.31 -     1.44: 2522
        1.44 -     1.57: 5046
        1.57 -     1.70: 13
        1.70 -     1.82: 90
  Bond restraints: 9120
  Sorted by residual:
  bond pdb=" CG  PHE R 174 "
       pdb=" CD1 PHE R 174 "
    ideal  model  delta    sigma   weight residual
    1.384  1.645 -0.261 2.10e-02 2.27e+03 1.55e+02
  bond pdb=" CA  SER B 161 "
       pdb=" CB  SER B 161 "
    ideal  model  delta    sigma   weight residual
    1.533  1.453  0.080 1.51e-02 4.39e+03 2.82e+01
  bond pdb=" CA  ALA B 106 "
       pdb=" CB  ALA B 106 "
    ideal  model  delta    sigma   weight residual
    1.530  1.450  0.079 1.58e-02 4.01e+03 2.53e+01
  bond pdb=" CB  LYS R 177 "
       pdb=" CG  LYS R 177 "
    ideal  model  delta    sigma   weight residual
    1.520  1.388  0.132 3.00e-02 1.11e+03 1.94e+01
  bond pdb=" CB  MET R 180 "
       pdb=" CG  MET R 180 "
    ideal  model  delta    sigma   weight residual
    1.520  1.397  0.123 3.00e-02 1.11e+03 1.69e+01
  ... (remaining 9115 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.42: 11834
        4.42 -     8.83: 492
        8.83 -    13.25: 34
       13.25 -    17.67: 5
       17.67 -    22.09: 4
  Bond angle restraints: 12369
  Sorted by residual:
  angle pdb=" CA  PHE B 151 "
        pdb=" CB  PHE B 151 "
        pdb=" CG  PHE B 151 "
      ideal   model   delta    sigma   weight residual
     113.80  130.28  -16.48 1.00e+00 1.00e+00 2.71e+02
  angle pdb=" O   ALA B 106 "
        pdb=" C   ALA B 106 "
        pdb=" N   PRO B 107 "
      ideal   model   delta    sigma   weight residual
     121.32  102.39   18.93 1.15e+00 7.56e-01 2.71e+02
  angle pdb=" CA  ALA B 106 "
        pdb=" C   ALA B 106 "
        pdb=" O   ALA B 106 "
      ideal   model   delta    sigma   weight residual
     120.16   98.07   22.09 1.37e+00 5.33e-01 2.60e+02
  angle pdb=" CB  PHE R 174 "
        pdb=" CG  PHE R 174 "
        pdb=" CD2 PHE R 174 "
      ideal   model   delta    sigma   weight residual
     120.70  140.24  -19.54 1.70e+00 3.46e-01 1.32e+02
  angle pdb=" C   ARG B  48 "
        pdb=" CA  ARG B  48 "
        pdb=" CB  ARG B  48 "
      ideal   model   delta    sigma   weight residual
     111.06  128.52  -17.46 1.55e+00 4.16e-01 1.27e+02
  ... (remaining 12364 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.25: 4832
       16.25 -    32.51: 396
       32.51 -    48.76: 121
       48.76 -    65.02: 34
       65.02 -    81.27: 9
  Dihedral angle restraints: 5392
    sinusoidal: 2044
      harmonic: 3348
  Sorted by residual:
  dihedral pdb=" C   ARG B  48 "
           pdb=" N   ARG B  48 "
           pdb=" CA  ARG B  48 "
           pdb=" CB  ARG B  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -146.56   23.96     0      2.50e+00 1.60e-01 9.18e+01
  dihedral pdb=" CB  CYS R 141 "
           pdb=" SG  CYS R 141 "
           pdb=" SG  CYS R 224 "
           pdb=" CB  CYS R 224 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.27   81.27     1      1.00e+01 1.00e-02 8.14e+01
  dihedral pdb=" C   ARG D 179 "
           pdb=" N   ARG D 179 "
           pdb=" CA  ARG D 179 "
           pdb=" CB  ARG D 179 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -144.36   21.76     0      2.50e+00 1.60e-01 7.58e+01
  ... (remaining 5389 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.164: 1233
       0.164 -    0.329: 164
       0.329 -    0.493: 15
       0.493 -    0.658: 3
       0.658 -    0.822: 2
  Chirality restraints: 1417
  Sorted by residual:
  chirality pdb=" CA  ARG B  48 "
            pdb=" N   ARG B  48 "
            pdb=" C   ARG B  48 "
            pdb=" CB  ARG B  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.69    0.82 2.00e-01 2.50e+01 1.69e+01
  chirality pdb=" CA  ARG D 179 "
            pdb=" N   ARG D 179 "
            pdb=" C   ARG D 179 "
            pdb=" CB  ARG D 179 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.70    0.81 2.00e-01 2.50e+01 1.64e+01
  chirality pdb=" CG  LEU R  71 "
            pdb=" CB  LEU R  71 "
            pdb=" CD1 LEU R  71 "
            pdb=" CD2 LEU R  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -3.22    0.63 2.00e-01 2.50e+01 9.96e+00
  ... (remaining 1414 not shown)

  Planarity restraints: 1560
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 106 "    0.096 2.00e-02 2.50e+03   1.62e-01 2.62e+02
        pdb=" C   ALA B 106 "   -0.279 2.00e-02 2.50e+03
        pdb=" O   ALA B 106 "    0.070 2.00e-02 2.50e+03
        pdb=" N   PRO B 107 "    0.113 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG R  90 "   -0.924 9.50e-02 1.11e+02   4.14e-01 1.04e+02
        pdb=" NE  ARG R  90 "    0.055 2.00e-02 2.50e+03
        pdb=" CZ  ARG R  90 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG R  90 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG R  90 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 174 "    0.015 2.00e-02 2.50e+03   5.23e-02 4.79e+01
        pdb=" CG  PHE R 174 "   -0.106 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 174 "    0.054 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 174 "    0.065 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 174 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 174 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 174 "   -0.025 2.00e-02 2.50e+03
  ... (remaining 1557 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 117
        2.65 -     3.22: 7202
        3.22 -     3.78: 12973
        3.78 -     4.34: 17678
        4.34 -     4.90: 29162
  Nonbonded interactions: 67132
  Sorted by model distance:
  nonbonded pdb=" O   TYR B 105 "
            pdb=" O   ALA B 106 "
     model   vdw
     2.092 3.040
  nonbonded pdb=" O   LEU D 162 "
            pdb=" O   ARG D 179 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" O   ASP R 112 "
            pdb=" OG1 THR R 115 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" O   ASP B 333 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OG1 THR B  29 "
            pdb=" OE1 GLN B  32 "
     model   vdw
     2.301 3.040
  ... (remaining 67127 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.010
  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:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.520
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8970
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      :  0.017   0.819   9122  Z= 0.985
  Angle     :  2.160  22.086  12373  Z= 1.427
  Chirality :  0.117   0.822   1417
  Planarity :  0.018   0.414   1560
  Dihedral  : 14.303  76.790   3226
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.59 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  6.14 %
    Allowed  :  7.28 %
    Favored  : 86.58 %
  Cbeta Deviations :  1.76 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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:  0.17 (0.22), residues: 1132
  helix:  1.25 (0.23), residues: 392
  sheet:  1.28 (0.36), residues: 170
  loop : -1.11 (0.22), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.070   0.008   ARG B 197 
 TYR   0.043   0.009   TYR B 111 
 PHE   0.106   0.008   PHE R 174 
 TRP   0.041   0.009   TRP D  47 
 HIS   0.024   0.006   HIS B 311 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01267 /  0.81 ( 9120)
  covalent geometry    : angle       2.15610 /  1.43 (12369)
  SS BOND              : bond        0.75663 / 37.65 (    2)
  SS BOND              : angle       7.69854 /  4.63 (    4)
  hydrogen bonds       : bond        0.26819 / 18.42 (  456)
  hydrogen bonds       : angle       6.72242 /  4.75 ( 1287)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 250
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  287 TYR cc_start: 0.8489 (m-10) cc_final: 0.8262 (m-80)
REVERT: A  328 ASP cc_start: 0.9139 (p0) cc_final: 0.8883 (p0)
REVERT: A  331 ASN cc_start: 0.9133 (m-40) cc_final: 0.8906 (m-40)
REVERT: B   15 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.8928 (tmmt)
REVERT: C   42 GLU cc_start: 0.9416 (mm-30) cc_final: 0.9117 (tm-30)
REVERT: D  211 ASP cc_start: 0.8754 (m-30) cc_final: 0.8380 (m-30)
REVERT: D  218 MET cc_start: 0.9073 (ttp) cc_final: 0.8783 (ttm)
REVERT: R  198 LEU cc_start: 0.8691 (mt) cc_final: 0.8435 (tt)
REVERT: R  209 GLU cc_start: 0.8609 (tt0) cc_final: 0.8306 (tp30)
REVERT: R  210 GLN cc_start: 0.7744 (tt0) cc_final: 0.7446 (tt0)
REVERT: R  333 GLN cc_start: 0.8105 (mt0) cc_final: 0.7849 (mp10)
  outliers start: 59
  outliers final: 9
  residues processed: 289
  average time/residue: 0.5457
  time to fit residues: 166.5617
Evaluate side-chains
  151 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 141
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue  160 THR
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue   99 SER
Chi-restraints excluded: chain R residue  165 GLU
Chi-restraints excluded: chain R residue  331 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    0.3980
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 269 ASN
A 333 GLN
B  75 GLN
B  88 ASN
B 259 GLN
B 311 HIS
C  18 GLN
D 182 ASN
R 126 ASN
R 261 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.103986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.069481 restraints weight = 17561.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 3.27
r_work: 0.2882 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.3893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9122  Z= 0.162
  Angle     :  0.720  11.383  12373  Z= 0.372
  Chirality :  0.045   0.151   1417
  Planarity :  0.004   0.046   1560
  Dihedral  :  5.933  55.067   1267
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 17.79 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  0.89 (0.23), residues: 1132
  helix:  2.12 (0.24), residues: 404
  sheet:  0.79 (0.30), residues: 258
  loop : -0.90 (0.25), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 208 
 TYR   0.019   0.002   TYR R 339 
 PHE   0.019   0.002   PHE C  61 
 TRP   0.019   0.002   TRP B 339 
 HIS   0.004   0.001   HIS R 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.16 ( 9120)
  covalent geometry    : angle       0.71974 /  0.37 (12369)
  SS BOND              : bond        0.01496 /  0.77 (    2)
  SS BOND              : angle       1.34161 /  0.73 (    4)
  hydrogen bonds       : bond        0.06946 /  4.74 (  456)
  hydrogen bonds       : angle       4.62451 /  3.28 ( 1287)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 166
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8456 (mm-30)
REVERT: A  313 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7746 (ptm160)
REVERT: A  328 ASP cc_start: 0.8741 (p0) cc_final: 0.8165 (p0)
REVERT: B    8 ARG cc_start: 0.9086 (tpp-160) cc_final: 0.8830 (mpt-90)
REVERT: B   15 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8627 (tmmt)
REVERT: B   19 ARG cc_start: 0.8773 (ttm170) cc_final: 0.8268 (ttp-110)
REVERT: B  215 GLU cc_start: 0.8002 (mp0) cc_final: 0.7783 (mp0)
REVERT: B  262 MET cc_start: 0.8523 (tpt) cc_final: 0.8295 (tpp)
REVERT: C   14 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8837 (mmpt)
REVERT: C   22 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8447 (mt-10)
REVERT: D  235 LEU cc_start: 0.7937 (pt) cc_final: 0.7730 (pp)
REVERT: R  120 MET cc_start: 0.8645 (tmm) cc_final: 0.8368 (tmm)
REVERT: R  207 MET cc_start: 0.9079 (mmm) cc_final: 0.8858 (mmm)
REVERT: R  209 GLU cc_start: 0.7676 (tt0) cc_final: 0.7303 (tp30)
  outliers start: 37
  outliers final: 7
  residues processed: 189
  average time/residue: 0.6515
  time to fit residues: 129.6926
Evaluate side-chains
  144 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 133
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ARG
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain C residue   14 LYS
Chi-restraints excluded: chain D residue  160 THR
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  122 VAL
Chi-restraints excluded: chain R residue  239 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   chunk 15 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9990
   chunk 51 optimal weight:    8.9990
   chunk 34 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 108 optimal weight:    7.9990
   chunk 69 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 331 ASN
A 333 GLN
B  75 GLN
R 211 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.101830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.067426 restraints weight = 17485.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 3.22
r_work: 0.2810 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.4431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9122  Z= 0.142
  Angle     :  0.639   9.368  12373  Z= 0.331
  Chirality :  0.043   0.139   1417
  Planarity :  0.004   0.035   1560
  Dihedral  :  4.987  53.439   1253
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 18.52 %
    Favored  : 78.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.24), residues: 1132
  helix:  2.45 (0.24), residues: 411
  sheet:  0.82 (0.31), residues: 269
  loop : -0.80 (0.26), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 268 
 TYR   0.018   0.001   TYR R 339 
 PHE   0.022   0.001   PHE B 151 
 TRP   0.010   0.001   TRP R 316 
 HIS   0.005   0.001   HIS R 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.14 ( 9120)
  covalent geometry    : angle       0.63875 /  0.33 (12369)
  SS BOND              : bond        0.00753 /  0.39 (    2)
  SS BOND              : angle       1.35205 /  0.74 (    4)
  hydrogen bonds       : bond        0.06120 /  4.19 (  456)
  hydrogen bonds       : angle       4.22080 /  3.01 ( 1287)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 148
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8247 (mm-30)
REVERT: A  306 GLN cc_start: 0.9404 (mm-40) cc_final: 0.9094 (mm110)
REVERT: B   44 GLN cc_start: 0.8546 (pm20) cc_final: 0.8181 (pm20)
REVERT: B  262 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8370 (tpp)
REVERT: C   14 LYS cc_start: 0.9268 (mmmm) cc_final: 0.8797 (mmpt)
REVERT: C   22 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8403 (mt-10)
REVERT: D  162 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8831 (tm)
REVERT: D  206 ARG cc_start: 0.8104 (ttp80) cc_final: 0.7629 (tmt-80)
REVERT: R  120 MET cc_start: 0.8649 (tmm) cc_final: 0.8393 (tmm)
REVERT: R  203 MET cc_start: 0.8413 (tpp) cc_final: 0.8208 (tpp)
  outliers start: 32
  outliers final: 15
  residues processed: 164
  average time/residue: 0.5470
  time to fit residues: 94.9223
Evaluate side-chains
  155 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue  160 THR
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  174 GLN
Chi-restraints excluded: chain D residue  183 LEU
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  183 SER
Chi-restraints excluded: chain R residue  239 VAL
Chi-restraints excluded: chain R residue  359 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 57 optimal weight:    0.2980
   chunk 62 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 90 optimal weight:    8.9990
   chunk 15 optimal weight:   10.0000
   chunk 104 optimal weight:    7.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 333 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.100250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.065610 restraints weight = 17753.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 3.20
r_work: 0.2793 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.4735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9122  Z= 0.134
  Angle     :  0.620  10.379  12373  Z= 0.319
  Chirality :  0.042   0.190   1417
  Planarity :  0.003   0.040   1560
  Dihedral  :  4.794  52.483   1249
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 19.67 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.24), residues: 1132
  helix:  2.60 (0.25), residues: 412
  sheet:  0.90 (0.32), residues: 269
  loop : -0.74 (0.26), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 268 
 TYR   0.017   0.001   TYR R 339 
 PHE   0.018   0.001   PHE B 151 
 TRP   0.009   0.001   TRP R 316 
 HIS   0.006   0.001   HIS R 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.13 ( 9120)
  covalent geometry    : angle       0.61990 /  0.32 (12369)
  SS BOND              : bond        0.00684 /  0.36 (    2)
  SS BOND              : angle       1.19479 /  0.65 (    4)
  hydrogen bonds       : bond        0.05659 /  3.88 (  456)
  hydrogen bonds       : angle       4.11222 /  2.94 ( 1287)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8186 (mm-30)
REVERT: A  276 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8200 (mm-30)
REVERT: A  306 GLN cc_start: 0.9444 (mm-40) cc_final: 0.9130 (mm110)
REVERT: B   19 ARG cc_start: 0.8851 (ttm170) cc_final: 0.8493 (ttp-110)
REVERT: B   44 GLN cc_start: 0.8494 (pm20) cc_final: 0.8170 (pm20)
REVERT: B  262 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8423 (tpp)
REVERT: C   14 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8851 (mmpt)
REVERT: C   22 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8407 (mt-10)
REVERT: D  162 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8852 (tm)
REVERT: D  206 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7698 (tmt-80)
REVERT: R  120 MET cc_start: 0.8598 (tmm) cc_final: 0.8310 (tmm)
REVERT: R  203 MET cc_start: 0.8518 (tpp) cc_final: 0.8292 (tpp)
  outliers start: 27
  outliers final: 13
  residues processed: 163
  average time/residue: 0.6408
  time to fit residues: 110.2893
Evaluate side-chains
  152 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain C residue   14 LYS
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue  160 THR
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  174 GLN
Chi-restraints excluded: chain D residue  183 LEU
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain R residue  183 SER
Chi-restraints excluded: chain R residue  239 VAL
Chi-restraints excluded: chain R residue  359 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 69 optimal weight:    1.9990
   chunk 108 optimal weight:    7.9990
   chunk 85 optimal weight:    7.9990
   chunk 48 optimal weight:    0.0670
   chunk 38 optimal weight:    1.9990
   chunk 110 optimal weight:    5.9990
   overall best weight:    1.4126

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 333 GLN
** R 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 320 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.097645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.062925 restraints weight = 17581.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 3.20
r_work: 0.2747 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.4869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9122  Z= 0.156
  Angle     :  0.649  10.535  12373  Z= 0.337
  Chirality :  0.043   0.191   1417
  Planarity :  0.004   0.041   1560
  Dihedral  :  4.679  50.418   1247
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 20.81 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.24), residues: 1132
  helix:  2.55 (0.25), residues: 413
  sheet:  1.00 (0.31), residues: 268
  loop : -0.90 (0.26), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B   8 
 TYR   0.017   0.001   TYR R 339 
 PHE   0.021   0.002   PHE B 151 
 TRP   0.011   0.001   TRP R 316 
 HIS   0.027   0.001   HIS R 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.16 ( 9120)
  covalent geometry    : angle       0.64833 /  0.34 (12369)
  SS BOND              : bond        0.00819 /  0.43 (    2)
  SS BOND              : angle       1.42654 /  0.77 (    4)
  hydrogen bonds       : bond        0.06147 /  4.20 (  456)
  hydrogen bonds       : angle       4.20824 /  3.00 ( 1287)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 144
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8659 (tpp) cc_final: 0.8182 (mtm)
REVERT: A  208 ARG cc_start: 0.8052 (mtm110) cc_final: 0.7543 (ttm-80)
REVERT: A  276 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8140 (mm-30)
REVERT: A  306 GLN cc_start: 0.9471 (mm-40) cc_final: 0.9158 (mm110)
REVERT: B   20 ASP cc_start: 0.9069 (m-30) cc_final: 0.8746 (m-30)
REVERT: B   32 GLN cc_start: 0.9151 (mt0) cc_final: 0.8841 (mp10)
REVERT: B   44 GLN cc_start: 0.8422 (pm20) cc_final: 0.8009 (pm20)
REVERT: B  262 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8453 (tpp)
REVERT: C   22 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8409 (mt-10)
REVERT: D  162 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8820 (tm)
REVERT: D  206 ARG cc_start: 0.8332 (ttp80) cc_final: 0.8063 (ttp80)
REVERT: R  120 MET cc_start: 0.8625 (tmm) cc_final: 0.8315 (tmm)
REVERT: R  207 MET cc_start: 0.9007 (mmm) cc_final: 0.8792 (mmm)
  outliers start: 28
  outliers final: 17
  residues processed: 163
  average time/residue: 0.6371
  time to fit residues: 109.6476
Evaluate side-chains
  154 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue  160 THR
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  174 GLN
Chi-restraints excluded: chain D residue  183 LEU
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain R residue  177 LYS
Chi-restraints excluded: chain R residue  183 SER
Chi-restraints excluded: chain R residue  239 VAL
Chi-restraints excluded: chain R residue  359 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 86 optimal weight:   20.0000
   chunk 61 optimal weight:    4.9990
   chunk 67 optimal weight:    6.9990
   chunk 29 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 99 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 108 optimal weight:    3.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 333 GLN
C  24 ASN
R 210 GLN
R 211 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.099108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.064637 restraints weight = 17599.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 3.20
r_work: 0.2776 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.5110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9122  Z= 0.129
  Angle     :  0.632  12.523  12373  Z= 0.321
  Chirality :  0.042   0.205   1417
  Planarity :  0.004   0.039   1560
  Dihedral  :  4.512  49.283   1247
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 21.64 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.24), residues: 1132
  helix:  2.60 (0.25), residues: 412
  sheet:  1.01 (0.31), residues: 268
  loop : -0.82 (0.26), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  13 
 TYR   0.016   0.001   TYR R 339 
 PHE   0.014   0.001   PHE B 151 
 TRP   0.011   0.001   TRP R 316 
 HIS   0.004   0.001   HIS R 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.13 ( 9120)
  covalent geometry    : angle       0.63157 /  0.32 (12369)
  SS BOND              : bond        0.00646 /  0.34 (    2)
  SS BOND              : angle       1.11275 /  0.60 (    4)
  hydrogen bonds       : bond        0.05372 /  3.69 (  456)
  hydrogen bonds       : angle       4.07011 /  2.92 ( 1287)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 144
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8640 (tpp) cc_final: 0.8205 (mtm)
REVERT: A  208 ARG cc_start: 0.7998 (mtm110) cc_final: 0.7465 (ttm-80)
REVERT: A  276 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8119 (mm-30)
REVERT: A  306 GLN cc_start: 0.9466 (mm-40) cc_final: 0.9140 (mm110)
REVERT: B   32 GLN cc_start: 0.9171 (mt0) cc_final: 0.8938 (mp10)
REVERT: B   44 GLN cc_start: 0.8454 (pm20) cc_final: 0.8144 (pm20)
REVERT: B  262 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8399 (tpp)
REVERT: C    9 ILE cc_start: 0.7710 (pp) cc_final: 0.7473 (pp)
REVERT: C   13 ARG cc_start: 0.8869 (ptp-110) cc_final: 0.8557 (mtm110)
REVERT: C   14 LYS cc_start: 0.9254 (mmmm) cc_final: 0.8821 (mmpt)
REVERT: D  162 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8838 (tm)
REVERT: D  206 ARG cc_start: 0.8334 (ttp80) cc_final: 0.8087 (ttp80)
REVERT: R  120 MET cc_start: 0.8624 (tmm) cc_final: 0.8296 (tmm)
REVERT: R  165 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8090 (mt-10)
  outliers start: 26
  outliers final: 14
  residues processed: 161
  average time/residue: 0.6160
  time to fit residues: 104.6333
Evaluate side-chains
  154 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 137
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue  160 THR
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  174 GLN
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain R residue  183 SER
Chi-restraints excluded: chain R residue  239 VAL
Chi-restraints excluded: chain R residue  300 HIS
Chi-restraints excluded: chain R residue  359 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9980
   chunk 94 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 37 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.9380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 333 GLN
C  24 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.098967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.064513 restraints weight = 17610.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.2899 rms_B_bonded: 3.20
r_work: 0.2773 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.5219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9122  Z= 0.131
  Angle     :  0.644  11.394  12373  Z= 0.326
  Chirality :  0.042   0.208   1417
  Planarity :  0.003   0.038   1560
  Dihedral  :  4.470  50.985   1247
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 22.48 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.41 (0.25), residues: 1132
  helix:  2.65 (0.25), residues: 412
  sheet:  1.07 (0.32), residues: 267
  loop : -0.82 (0.26), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 148 
 TYR   0.016   0.001   TYR R 339 
 PHE   0.015   0.001   PHE B 151 
 TRP   0.012   0.001   TRP R 316 
 HIS   0.006   0.001   HIS R 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.13 ( 9120)
  covalent geometry    : angle       0.64396 /  0.33 (12369)
  SS BOND              : bond        0.00664 /  0.35 (    2)
  SS BOND              : angle       1.17770 /  0.64 (    4)
  hydrogen bonds       : bond        0.05304 /  3.64 (  456)
  hydrogen bonds       : angle       4.05670 /  2.91 ( 1287)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8150 (mm-30)
REVERT: A   53 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8301 (mtm)
REVERT: A  208 ARG cc_start: 0.8025 (mtm110) cc_final: 0.7506 (ttm-80)
REVERT: A  306 GLN cc_start: 0.9474 (mm-40) cc_final: 0.9145 (mm110)
REVERT: A  313 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8132 (ptm160)
REVERT: B   32 GLN cc_start: 0.9210 (mt0) cc_final: 0.8869 (mp10)
REVERT: B   42 ARG cc_start: 0.7654 (ttt180) cc_final: 0.7363 (tmt170)
REVERT: B   44 GLN cc_start: 0.8440 (pm20) cc_final: 0.7934 (pm20)
REVERT: B  217 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7449 (pmt)
REVERT: B  262 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8413 (tpp)
REVERT: D  162 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8836 (tm)
REVERT: D  206 ARG cc_start: 0.8350 (ttp80) cc_final: 0.8072 (ttp80)
REVERT: R  120 MET cc_start: 0.8577 (tmm) cc_final: 0.8266 (tmm)
  outliers start: 27
  outliers final: 17
  residues processed: 159
  average time/residue: 0.5913
  time to fit residues: 99.1140
Evaluate side-chains
  158 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain D residue  160 THR
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  174 GLN
Chi-restraints excluded: chain D residue  183 LEU
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain R residue  122 VAL
Chi-restraints excluded: chain R residue  239 VAL
Chi-restraints excluded: chain R residue  331 ASP
Chi-restraints excluded: chain R residue  359 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 68 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 90 optimal weight:    0.4980
   chunk 27 optimal weight:    0.0370
   chunk 75 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9980
   chunk 94 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    0.6258

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 333 GLN
C  24 ASN
R 211 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.100227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.065820 restraints weight = 17634.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 3.21
r_work: 0.2803 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.5382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9122  Z= 0.122
  Angle     :  0.653  11.787  12373  Z= 0.325
  Chirality :  0.042   0.243   1417
  Planarity :  0.003   0.036   1560
  Dihedral  :  4.375  52.715   1247
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 23.52 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.46 (0.25), residues: 1132
  helix:  2.67 (0.25), residues: 412
  sheet:  1.02 (0.31), residues: 269
  loop : -0.72 (0.26), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B   8 
 TYR   0.016   0.001   TYR R 339 
 PHE   0.012   0.001   PHE B 151 
 TRP   0.012   0.001   TRP R 316 
 HIS   0.006   0.001   HIS R 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.12 ( 9120)
  covalent geometry    : angle       0.65254 /  0.33 (12369)
  SS BOND              : bond        0.00569 /  0.30 (    2)
  SS BOND              : angle       0.97334 /  0.53 (    4)
  hydrogen bonds       : bond        0.04765 /  3.28 (  456)
  hydrogen bonds       : angle       3.96533 /  2.84 ( 1287)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8102 (mm-30)
REVERT: A   53 MET cc_start: 0.8645 (tpp) cc_final: 0.8308 (mtm)
REVERT: A  208 ARG cc_start: 0.7957 (mtm110) cc_final: 0.7438 (ttm-80)
REVERT: A  286 CYS cc_start: 0.8519 (t) cc_final: 0.8026 (t)
REVERT: A  306 GLN cc_start: 0.9469 (mm-40) cc_final: 0.9130 (mm110)
REVERT: A  313 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8045 (ptm160)
REVERT: A  328 ASP cc_start: 0.8816 (p0) cc_final: 0.8569 (m-30)
REVERT: B   44 GLN cc_start: 0.8435 (pm20) cc_final: 0.8069 (pm20)
REVERT: B  217 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7439 (pmt)
REVERT: B  234 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.7765 (t80)
REVERT: B  262 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8408 (tpp)
REVERT: B  323 ASP cc_start: 0.8737 (m-30) cc_final: 0.8512 (p0)
REVERT: D  162 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8825 (tm)
REVERT: D  206 ARG cc_start: 0.8359 (ttp80) cc_final: 0.8090 (ttp80)
REVERT: R  120 MET cc_start: 0.8555 (tmm) cc_final: 0.8261 (tmm)
REVERT: R  165 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8112 (mt-10)
  outliers start: 22
  outliers final: 11
  residues processed: 155
  average time/residue: 0.5621
  time to fit residues: 92.2158
Evaluate side-chains
  152 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain D residue  160 THR
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  174 GLN
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain D residue  233 LEU
Chi-restraints excluded: chain R residue  177 LYS
Chi-restraints excluded: chain R residue  239 VAL
Chi-restraints excluded: chain R residue  359 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 99 optimal weight:   10.0000
   chunk 89 optimal weight:    4.9990
   chunk 59 optimal weight:    0.0570
   chunk 29 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 83 optimal weight:    6.9990
   chunk 8 optimal weight:    0.4980
   chunk 46 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.9104

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 333 GLN
** B  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  24 ASN
** R 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 350 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.099261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.064568 restraints weight = 17613.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 3.21
r_work: 0.2776 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.5401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9122  Z= 0.133
  Angle     :  0.682  12.176  12373  Z= 0.344
  Chirality :  0.043   0.247   1417
  Planarity :  0.004   0.036   1560
  Dihedral  :  4.405  53.198   1247
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 24.35 %
    Favored  : 73.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.24), residues: 1132
  helix:  2.56 (0.25), residues: 412
  sheet:  1.17 (0.31), residues: 265
  loop : -0.76 (0.26), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 148 
 TYR   0.016   0.001   TYR R 339 
 PHE   0.015   0.001   PHE B 151 
 TRP   0.011   0.001   TRP R 316 
 HIS   0.010   0.001   HIS R 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 ( 9120)
  covalent geometry    : angle       0.68200 /  0.34 (12369)
  SS BOND              : bond        0.00638 /  0.34 (    2)
  SS BOND              : angle       1.13699 /  0.62 (    4)
  hydrogen bonds       : bond        0.05046 /  3.47 (  456)
  hydrogen bonds       : angle       4.03506 /  2.90 ( 1287)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 141
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8115 (mm-30)
REVERT: A   53 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8355 (mtm)
REVERT: A  208 ARG cc_start: 0.8003 (mtm110) cc_final: 0.7491 (ttm-80)
REVERT: A  286 CYS cc_start: 0.8505 (t) cc_final: 0.8036 (t)
REVERT: A  306 GLN cc_start: 0.9431 (mm-40) cc_final: 0.9100 (mm110)
REVERT: A  313 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8102 (ptm160)
REVERT: A  328 ASP cc_start: 0.8816 (p0) cc_final: 0.8540 (m-30)
REVERT: B   44 GLN cc_start: 0.8425 (pm20) cc_final: 0.7961 (pm20)
REVERT: B  217 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7443 (pmt)
REVERT: B  262 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8433 (tpp)
REVERT: B  323 ASP cc_start: 0.8724 (m-30) cc_final: 0.8448 (p0)
REVERT: D  162 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8817 (tm)
REVERT: D  206 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8119 (ttp80)
REVERT: R  120 MET cc_start: 0.8544 (tmm) cc_final: 0.8248 (tmm)
REVERT: R  165 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8107 (mt-10)
  outliers start: 19
  outliers final: 14
  residues processed: 151
  average time/residue: 0.5479
  time to fit residues: 87.2387
Evaluate side-chains
  156 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain D residue  160 THR
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  174 GLN
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain R residue  122 VAL
Chi-restraints excluded: chain R residue  239 VAL
Chi-restraints excluded: chain R residue  331 ASP
Chi-restraints excluded: chain R residue  359 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0000
   chunk 1 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0170
   chunk 50 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   overall best weight:    0.5624

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 333 GLN
C  24 ASN
** R 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 211 ASN
R 350 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.100946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.066123 restraints weight = 17627.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 3.22
r_work: 0.2820 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.5536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9122  Z= 0.123
  Angle     :  0.674  13.688  12373  Z= 0.338
  Chirality :  0.042   0.246   1417
  Planarity :  0.004   0.036   1560
  Dihedral  :  4.344  53.666   1247
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 24.77 %
    Favored  : 73.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.25), residues: 1132
  helix:  2.63 (0.25), residues: 412
  sheet:  1.25 (0.31), residues: 263
  loop : -0.71 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 148 
 TYR   0.016   0.001   TYR R 339 
 PHE   0.011   0.001   PHE B 151 
 TRP   0.011   0.001   TRP R 316 
 HIS   0.009   0.001   HIS R 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.12 ( 9120)
  covalent geometry    : angle       0.67356 /  0.34 (12369)
  SS BOND              : bond        0.00553 /  0.29 (    2)
  SS BOND              : angle       0.94119 /  0.52 (    4)
  hydrogen bonds       : bond        0.04609 /  3.17 (  456)
  hydrogen bonds       : angle       3.96340 /  2.85 ( 1287)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 143
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8133 (mm-30)
REVERT: A   53 MET cc_start: 0.8658 (tpp) cc_final: 0.8361 (mtm)
REVERT: A  208 ARG cc_start: 0.8016 (mtm110) cc_final: 0.7497 (ttm-80)
REVERT: A  286 CYS cc_start: 0.8526 (t) cc_final: 0.7964 (t)
REVERT: A  306 GLN cc_start: 0.9423 (mm-40) cc_final: 0.9045 (mm110)
REVERT: A  313 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8077 (ptm160)
REVERT: A  328 ASP cc_start: 0.8812 (p0) cc_final: 0.8520 (m-30)
REVERT: B   42 ARG cc_start: 0.7575 (tmt170) cc_final: 0.7170 (tmt170)
REVERT: B   44 GLN cc_start: 0.8302 (pm20) cc_final: 0.7794 (pm20)
REVERT: B  217 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7459 (pmt)
REVERT: B  234 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.7804 (t80)
REVERT: B  262 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8434 (tpp)
REVERT: C   13 ARG cc_start: 0.8953 (ptp-110) cc_final: 0.8696 (mtm110)
REVERT: C   14 LYS cc_start: 0.9249 (mmmm) cc_final: 0.8809 (mmpt)
REVERT: D  162 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8826 (tm)
REVERT: D  206 ARG cc_start: 0.8356 (ttp80) cc_final: 0.8086 (ttp80)
REVERT: R  120 MET cc_start: 0.8511 (tmm) cc_final: 0.8198 (tmm)
REVERT: R  165 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8086 (mt-10)
REVERT: R  234 LYS cc_start: 0.7658 (ttmm) cc_final: 0.7272 (mtpp)
  outliers start: 17
  outliers final: 9
  residues processed: 151
  average time/residue: 0.6298
  time to fit residues: 100.3917
Evaluate side-chains
  153 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain D residue  160 THR
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  174 GLN
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain R residue  239 VAL
Chi-restraints excluded: chain R residue  359 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 19 optimal weight:    0.4980
   chunk 85 optimal weight:    2.9990
   chunk 110 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9990
   chunk 107 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 72 optimal weight:    4.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 333 GLN
C  24 ASN
** R 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 350 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.098087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.063389 restraints weight = 17536.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.2895 rms_B_bonded: 3.19
r_work: 0.2767 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.5444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9122  Z= 0.153
  Angle     :  0.712  13.764  12373  Z= 0.361
  Chirality :  0.044   0.235   1417
  Planarity :  0.004   0.036   1560
  Dihedral  :  4.475  52.903   1247
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 24.56 %
    Favored  : 73.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.41 (0.25), residues: 1132
  helix:  2.52 (0.25), residues: 412
  sheet:  1.29 (0.31), residues: 267
  loop : -0.84 (0.26), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 148 
 TYR   0.016   0.001   TYR A 296 
 PHE   0.017   0.001   PHE B 151 
 TRP   0.010   0.001   TRP R 316 
 HIS   0.009   0.001   HIS R 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00357 /  0.15 ( 9120)
  covalent geometry    : angle       0.71147 /  0.36 (12369)
  SS BOND              : bond        0.00752 /  0.40 (    2)
  SS BOND              : angle       1.29281 /  0.70 (    4)
  hydrogen bonds       : bond        0.05534 /  3.78 (  456)
  hydrogen bonds       : angle       4.13145 /  2.96 ( 1287)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3545.99 seconds
wall clock time: 61 minutes 0.75 seconds (3660.75 seconds total)