Starting phenix.real_space_refine
on Fri Aug 22 17:39:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8unl_42408/08_2025/8unl_42408.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8unl_42408/08_2025/8unl_42408.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8unl_42408/08_2025/8unl_42408.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8unl_42408/08_2025/8unl_42408.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8unl_42408/08_2025/8unl_42408.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8unl_42408/08_2025/8unl_42408.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.027
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: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      40      5.16       5
     C    4219      2.51       5
     N    1122      2.21       5
     O    1166      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6550
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1692
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1692
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 61}
          Link IDs: {'PTRANS': 5, 'TRANS': 225}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 234
          Unresolved non-hydrogen angles: 282
          Unresolved non-hydrogen dihedrals: 188
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ARG:plan': 10, 'ASN:plan1': 2, 'GLU:plan': 14, 'GLN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 161
    Chain: "B"
      Number of atoms: 2400
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 332, 2400
          Classifications: {'peptide': 332}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 5, 'TRANS': 326}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 152
          Unresolved non-hydrogen angles: 185
          Unresolved non-hydrogen dihedrals: 119
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 11, 'GLN:plan1': 5, 'ARG:plan': 8, 'GLU:plan': 4, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 118
    Chain: "G"
      Number of atoms: 320
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 320
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 92
          Unresolved non-hydrogen dihedrals: 66
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 38
    Chain: "R"
      Number of atoms: 2090
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2090
          Classifications: {'peptide': 280}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PTRANS': 7, 'TRANS': 272}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 168
          Unresolved non-hydrogen angles: 203
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 9, 'GLN:plan1': 5, 'ASP:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 4, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 107
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 16
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 1.34, per 1000 atoms: 0.20
  Number of scatterers: 6550
  At special positions: 0
  Unit cell: (83.2992, 134.493, 97.1824, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     P       3     15.00
     O    1166      8.00
     N    1122      7.00
     C    4219      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 333.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1696

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 8 sheets defined
      47.8% alpha, 17.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 40
      removed outlier: 3.876A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   THR A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 63
      removed outlier: 3.506A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 239
      removed outlier: 3.864A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 295 through 302
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.829A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 3.790A  pdb=" N   TYR A 318 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.505A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 6 through 26
      removed outlier: 3.815A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   LEU B  14 " --> pdb=" O   GLU B  10 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LYS B  15 " --> pdb=" O   ALA B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.516A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 13 through 24
      removed outlier: 3.854A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.518A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 37 through 61
      removed outlier: 3.538A  pdb=" N   GLY R  50 " --> pdb=" O   ALA R  46 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 3.525A  pdb=" N   TYR R  70 " --> pdb=" O   THR R  66 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.926A  pdb=" N   ILE R 121 " --> pdb=" O   VAL R 117 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLU R 122 " --> pdb=" O   THR R 118 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   THR R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
      removed outlier: 3.536A  pdb=" N   LEU R 145 " --> pdb=" O   TYR R 141 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 166
      removed outlier: 3.608A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU R 155 " --> pdb=" O   ARG R 151 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   SER R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 166 through 171
      removed outlier: 3.576A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 172 through 175
      removed outlier: 3.546A  pdb=" N   ARG R 175 " --> pdb=" O   HIS R 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 172 through 175'
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 209 through 238
      removed outlier: 3.872A  pdb=" N   VAL R 213 " --> pdb=" O   TYR R 209 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ILE R 214 " --> pdb=" O   VAL R 210 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   MET R 215 " --> pdb=" O   PRO R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 299
      removed outlier: 3.821A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 4.489A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 318
      removed outlier: 3.538A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 321 through 327
    Processing helix  chain 'R' and resid 329 through 339
      removed outlier: 3.575A  pdb=" N   LEU R 339 " --> pdb=" O   ALA R 335 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 7.218A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.267A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.709A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.190A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.436A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.656A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.094A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.912A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.421A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.973A  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 150
      removed outlier: 6.878A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.713A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.586A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.699A  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: 3.869A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)

    344 hydrogen bonds defined for protein.
    1005 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: 1.01

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1033
        1.32 -     1.44: 1900
        1.44 -     1.56: 3696
        1.56 -     1.69: 7
        1.69 -     1.81: 54
  Bond restraints: 6690
  Sorted by residual:
  bond pdb=" CA  THR A 320 "
       pdb=" C   THR A 320 "
    ideal  model  delta    sigma   weight residual
    1.528  1.468  0.060 1.18e-02 7.18e+03 2.60e+01
  bond pdb=" CA  ASN R 148 "
       pdb=" C   ASN R 148 "
    ideal  model  delta    sigma   weight residual
    1.523  1.458  0.065 1.30e-02 5.92e+03 2.50e+01
  bond pdb=" CA  LEU R 145 "
       pdb=" C   LEU R 145 "
    ideal  model  delta    sigma   weight residual
    1.523  1.463  0.060 1.23e-02 6.61e+03 2.34e+01
  bond pdb=" C5  GTP A 401 "
       pdb=" C6  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.476 -0.086 2.00e-02 2.50e+03 1.86e+01
  bond pdb=" CA  GLN A  59 "
       pdb=" C   GLN A  59 "
    ideal  model  delta    sigma   weight residual
    1.524  1.475  0.048 1.27e-02 6.20e+03 1.45e+01
  ... (remaining 6685 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 9019
        2.36 -     4.71: 95
        4.71 -     7.07: 31
        7.07 -     9.42: 6
        9.42 -    11.78: 3
  Bond angle restraints: 9154
  Sorted by residual:
  angle pdb=" N   SER A 352 "
        pdb=" CA  SER A 352 "
        pdb=" C   SER A 352 "
      ideal   model   delta    sigma   weight residual
     111.28  123.06  -11.78 1.09e+00 8.42e-01 1.17e+02
  angle pdb=" N   ALA A 351 "
        pdb=" CA  ALA A 351 "
        pdb=" C   ALA A 351 "
      ideal   model   delta    sigma   weight residual
     111.28  118.61   -7.33 1.09e+00 8.42e-01 4.53e+01
  angle pdb=" N   THR A 320 "
        pdb=" CA  THR A 320 "
        pdb=" C   THR A 320 "
      ideal   model   delta    sigma   weight residual
     110.08  101.63    8.45 1.38e+00 5.25e-01 3.75e+01
  angle pdb=" N   SER R 143 "
        pdb=" CA  SER R 143 "
        pdb=" C   SER R 143 "
      ideal   model   delta    sigma   weight residual
     111.28  117.78   -6.50 1.09e+00 8.42e-01 3.56e+01
  angle pdb=" N   THR R 146 "
        pdb=" CA  THR R 146 "
        pdb=" C   THR R 146 "
      ideal   model   delta    sigma   weight residual
     109.50  100.99    8.51 1.58e+00 4.01e-01 2.90e+01
  ... (remaining 9149 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.00: 3780
       31.00 -    62.01: 71
       62.01 -    93.01: 2
       93.01 -   124.02: 0
      124.02 -   155.02: 5
  Dihedral angle restraints: 3858
    sinusoidal: 1250
      harmonic: 2608
  Sorted by residual:
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -50.43  155.02     1      2.00e+01 2.50e-03 4.58e+01
  dihedral pdb=" C4' GTP A 401 "
           pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     260.87  124.05  136.82     1      2.00e+01 2.50e-03 4.15e+01
  dihedral pdb=" O5' GTP A 401 "
           pdb=" O3A GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" PB  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -85.88   44.74 -130.62     1      2.00e+01 2.50e-03 3.96e+01
  ... (remaining 3855 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 838
       0.046 -    0.091: 205
       0.091 -    0.137: 57
       0.137 -    0.182: 4
       0.182 -    0.228: 1
  Chirality restraints: 1105
  Sorted by residual:
  chirality pdb=" CA  SER A 352 "
            pdb=" N   SER A 352 "
            pdb=" C   SER A 352 "
            pdb=" CB  SER A 352 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CA  HIS A 357 "
            pdb=" N   HIS A 357 "
            pdb=" C   HIS A 357 "
            pdb=" CB  HIS A 357 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.67e-01
  chirality pdb=" CA  ILE A  62 "
            pdb=" N   ILE A  62 "
            pdb=" C   ILE A  62 "
            pdb=" CB  ILE A  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.66e-01
  ... (remaining 1102 not shown)

  Planarity restraints: 1138
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 360 "   -0.070 5.00e-02 4.00e+02   1.10e-01 1.93e+01
        pdb=" N   PRO A 361 "    0.190 5.00e-02 4.00e+02
        pdb=" CA  PRO A 361 "   -0.059 5.00e-02 4.00e+02
        pdb=" CD  PRO A 361 "   -0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 360 "    0.022 2.00e-02 2.50e+03   4.35e-02 1.89e+01
        pdb=" C   TYR A 360 "   -0.075 2.00e-02 2.50e+03
        pdb=" O   TYR A 360 "    0.028 2.00e-02 2.50e+03
        pdb=" N   PRO A 361 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 320 "    0.035 5.00e-02 4.00e+02   5.22e-02 4.37e+00
        pdb=" N   PRO A 321 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 321 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 321 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1135 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1070
        2.76 -     3.30: 6023
        3.30 -     3.83: 10314
        3.83 -     4.37: 11100
        4.37 -     4.90: 21096
  Nonbonded interactions: 49603
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B  86 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OD2 ASP R 113 "
            pdb=" OAM G1I R 501 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OD1 ASP R 113 "
            pdb=" OH  TYR R 316 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" OH  TYR R 209 "
            pdb=" O   PHE R 290 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.344 3.040
  ... (remaining 49598 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.440
  Find NCS groups from input model:        0.030
  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:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
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      :  0.005   0.086   6691  Z= 0.313
  Angle     :  0.679  11.780   9156  Z= 0.419
  Chirality :  0.043   0.228   1105
  Planarity :  0.005   0.110   1138
  Dihedral  : 14.030 155.022   2159
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.49 (0.29), residues: 874
  helix:  2.56 (0.27), residues: 380
  sheet:  0.66 (0.43), residues: 160
  loop : -0.74 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 175 
 TYR   0.011   0.001   TYR R 141 
 PHE   0.010   0.001   PHE R  49 
 TRP   0.005   0.001   TRP R 313 
 HIS   0.011   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 6690)
  covalent geometry    : angle       0.67932 ( 9154)
  SS BOND              : bond        0.00025 (    1)
  SS BOND              : angle       0.17178 (    2)
  hydrogen bonds       : bond        0.17948 (  344)
  hydrogen bonds       : angle       6.47576 ( 1005)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A  350 THR cc_start: 0.8696 (m) cc_final: 0.8468 (p)
REVERT: A  369 THR cc_start: 0.8647 (p) cc_final: 0.8419 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0664
  time to fit residues: 8.0169
Evaluate side-chains
  74 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 340 ASN
R 103 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.123109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.104089 restraints weight = 9670.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 1.62
r_work: 0.3073 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.0887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6691  Z= 0.120
  Angle     :  0.473   5.820   9156  Z= 0.255
  Chirality :  0.040   0.138   1105
  Planarity :  0.003   0.037   1138
  Dihedral  :  9.511 145.282    975
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  7.12 %
    Favored  : 91.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.29), residues: 874
  helix:  2.59 (0.27), residues: 394
  sheet:  0.94 (0.45), residues: 146
  loop : -0.78 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 175 
 TYR   0.017   0.001   TYR A 358 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.008   0.001   TRP B 297 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6690)
  covalent geometry    : angle       0.47299 ( 9154)
  SS BOND              : bond        0.00095 (    1)
  SS BOND              : angle       0.43109 (    2)
  hydrogen bonds       : bond        0.04572 (  344)
  hydrogen bonds       : angle       4.47838 ( 1005)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.287 
Fit side-chains
REVERT: B  258 ASP cc_start: 0.8690 (t0) cc_final: 0.8418 (t0)
REVERT: R   82 MET cc_start: 0.8453 (ttm) cc_final: 0.8175 (ttp)
  outliers start: 8
  outliers final: 6
  residues processed: 78
  average time/residue: 0.0650
  time to fit residues: 7.5453
Evaluate side-chains
  77 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0020
   overall best weight:    1.3592

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.120119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.100755 restraints weight = 9750.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 1.65
r_work: 0.3043 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.1205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   6691  Z= 0.150
  Angle     :  0.486   5.435   9156  Z= 0.261
  Chirality :  0.041   0.142   1105
  Planarity :  0.003   0.039   1138
  Dihedral  :  8.270 142.054    975
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 2.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  8.61 %
    Favored  : 90.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.29), residues: 874
  helix:  2.53 (0.27), residues: 394
  sheet:  0.60 (0.42), residues: 163
  loop : -0.78 (0.33), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 175 
 TYR   0.019   0.001   TYR B  59 
 PHE   0.013   0.001   PHE B 241 
 TRP   0.009   0.001   TRP B 211 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 6690)
  covalent geometry    : angle       0.48638 ( 9154)
  SS BOND              : bond        0.00162 (    1)
  SS BOND              : angle       0.61427 (    2)
  hydrogen bonds       : bond        0.04724 (  344)
  hydrogen bonds       : angle       4.21468 ( 1005)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.232 
Fit side-chains
REVERT: B  258 ASP cc_start: 0.8765 (t0) cc_final: 0.8475 (t0)
REVERT: R   82 MET cc_start: 0.8496 (ttm) cc_final: 0.8215 (ttp)
  outliers start: 8
  outliers final: 7
  residues processed: 73
  average time/residue: 0.0588
  time to fit residues: 6.4282
Evaluate side-chains
  73 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 77 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0040
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.123975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.105099 restraints weight = 9794.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.3169 rms_B_bonded: 1.62
r_work: 0.3082 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.1275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6691  Z= 0.096
  Angle     :  0.426   5.619   9156  Z= 0.230
  Chirality :  0.040   0.133   1105
  Planarity :  0.003   0.038   1138
  Dihedral  :  7.488 135.791    975
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 2.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 10.60 %
    Favored  : 88.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.30), residues: 874
  helix:  2.65 (0.27), residues: 395
  sheet:  0.61 (0.42), residues: 158
  loop : -0.75 (0.33), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 175 
 TYR   0.011   0.001   TYR A 358 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.007   0.001   TRP B 297 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 ( 6690)
  covalent geometry    : angle       0.42570 ( 9154)
  SS BOND              : bond        0.00001 (    1)
  SS BOND              : angle       0.24707 (    2)
  hydrogen bonds       : bond        0.03628 (  344)
  hydrogen bonds       : angle       3.91833 ( 1005)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.253 
Fit side-chains
REVERT: B  258 ASP cc_start: 0.8705 (t0) cc_final: 0.8432 (t0)
REVERT: R   82 MET cc_start: 0.8396 (ttm) cc_final: 0.8046 (ttp)
  outliers start: 6
  outliers final: 5
  residues processed: 77
  average time/residue: 0.0661
  time to fit residues: 7.4162
Evaluate side-chains
  72 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 63 optimal weight:    0.0070
   chunk 68 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 61 optimal weight:    0.1980
   chunk 47 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   overall best weight:    0.7602

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.123695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.103623 restraints weight = 9971.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 1.87
r_work: 0.3052 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2932 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.1367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6691  Z= 0.102
  Angle     :  0.430   5.521   9156  Z= 0.232
  Chirality :  0.040   0.134   1105
  Planarity :  0.003   0.037   1138
  Dihedral  :  7.125 132.168    975
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 11.26 %
    Favored  : 87.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.29), residues: 874
  helix:  2.66 (0.27), residues: 395
  sheet:  0.72 (0.42), residues: 156
  loop : -0.78 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 175 
 TYR   0.011   0.001   TYR B  59 
 PHE   0.011   0.001   PHE B 241 
 TRP   0.007   0.001   TRP B 211 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 6690)
  covalent geometry    : angle       0.42984 ( 9154)
  SS BOND              : bond        0.00028 (    1)
  SS BOND              : angle       0.30915 (    2)
  hydrogen bonds       : bond        0.03762 (  344)
  hydrogen bonds       : angle       3.83874 ( 1005)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.252 
Fit side-chains
REVERT: B  258 ASP cc_start: 0.8756 (t0) cc_final: 0.8418 (t0)
REVERT: R   82 MET cc_start: 0.8426 (ttm) cc_final: 0.8027 (ttp)
  outliers start: 8
  outliers final: 6
  residues processed: 76
  average time/residue: 0.0611
  time to fit residues: 7.0961
Evaluate side-chains
  75 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 84 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   overall best weight:    1.0984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.122057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.102112 restraints weight = 9880.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 1.84
r_work: 0.3029 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6691  Z= 0.127
  Angle     :  0.458   5.480   9156  Z= 0.249
  Chirality :  0.041   0.138   1105
  Planarity :  0.003   0.038   1138
  Dihedral  :  6.962 131.110    975
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 11.42 %
    Favored  : 86.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.55 (0.29), residues: 874
  helix:  2.60 (0.27), residues: 394
  sheet:  0.69 (0.43), residues: 156
  loop : -0.83 (0.33), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 175 
 TYR   0.012   0.001   TYR B  59 
 PHE   0.013   0.001   PHE B 241 
 TRP   0.008   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6690)
  covalent geometry    : angle       0.45788 ( 9154)
  SS BOND              : bond        0.00111 (    1)
  SS BOND              : angle       0.49437 (    2)
  hydrogen bonds       : bond        0.04198 (  344)
  hydrogen bonds       : angle       3.89496 ( 1005)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.217 
Fit side-chains
REVERT: B  258 ASP cc_start: 0.8793 (t0) cc_final: 0.8445 (t0)
REVERT: R   82 MET cc_start: 0.8555 (ttm) cc_final: 0.8148 (ttp)
  outliers start: 10
  outliers final: 8
  residues processed: 80
  average time/residue: 0.0592
  time to fit residues: 7.1611
Evaluate side-chains
  78 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 23 optimal weight:   30.0000
   chunk 35 optimal weight:    0.0040
   chunk 69 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 14 optimal weight:    0.1980
   chunk 74 optimal weight:    0.0770
   chunk 61 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0370
   chunk 26 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   overall best weight:    0.2228

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.127553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.107468 restraints weight = 9705.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 1.86
r_work: 0.3127 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.019   6691  Z= 0.076
  Angle     :  0.411   7.924   9156  Z= 0.219
  Chirality :  0.039   0.131   1105
  Planarity :  0.002   0.037   1138
  Dihedral  :  6.410 122.193    975
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 12.91 %
    Favored  : 86.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.73 (0.30), residues: 874
  helix:  2.74 (0.27), residues: 395
  sheet:  0.79 (0.43), residues: 156
  loop : -0.74 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 175 
 TYR   0.007   0.001   TYR A 358 
 PHE   0.010   0.001   PHE B 241 
 TRP   0.007   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00145 ( 6690)
  covalent geometry    : angle       0.41129 ( 9154)
  SS BOND              : bond        0.00147 (    1)
  SS BOND              : angle       0.13511 (    2)
  hydrogen bonds       : bond        0.02676 (  344)
  hydrogen bonds       : angle       3.62748 ( 1005)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.219 
Fit side-chains
REVERT: B  258 ASP cc_start: 0.8665 (t0) cc_final: 0.8342 (t0)
  outliers start: 4
  outliers final: 4
  residues processed: 92
  average time/residue: 0.0547
  time to fit residues: 7.3741
Evaluate side-chains
  81 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   66 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 72 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9990
   chunk 58 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0270
   chunk 51 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.7038

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

Flipped N/Q/H residues before XYZ refinement:
A 384 GLN
B  32 GLN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.124337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.103769 restraints weight = 9797.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 1.94
r_work: 0.3081 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6691  Z= 0.096
  Angle     :  0.430   6.940   9156  Z= 0.227
  Chirality :  0.040   0.132   1105
  Planarity :  0.002   0.036   1138
  Dihedral  :  6.250 120.285    975
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 13.58 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.76 (0.30), residues: 874
  helix:  2.78 (0.27), residues: 395
  sheet:  0.74 (0.43), residues: 157
  loop : -0.72 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 175 
 TYR   0.008   0.001   TYR R 308 
 PHE   0.012   0.001   PHE B 241 
 TRP   0.007   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 6690)
  covalent geometry    : angle       0.43021 ( 9154)
  SS BOND              : bond        0.00021 (    1)
  SS BOND              : angle       0.24870 (    2)
  hydrogen bonds       : bond        0.03387 (  344)
  hydrogen bonds       : angle       3.66868 ( 1005)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.149 
Fit side-chains
REVERT: B  258 ASP cc_start: 0.8675 (t0) cc_final: 0.8324 (t0)
  outliers start: 8
  outliers final: 7
  residues processed: 77
  average time/residue: 0.0547
  time to fit residues: 6.3469
Evaluate side-chains
  80 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 68 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B  75 GLN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.123845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.102922 restraints weight = 9846.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 1.97
r_work: 0.3067 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6691  Z= 0.104
  Angle     :  0.437   6.908   9156  Z= 0.231
  Chirality :  0.040   0.133   1105
  Planarity :  0.003   0.036   1138
  Dihedral  :  6.202 119.152    975
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 13.74 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.30), residues: 874
  helix:  2.76 (0.27), residues: 395
  sheet:  0.72 (0.43), residues: 157
  loop : -0.72 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 175 
 TYR   0.008   0.001   TYR R 308 
 PHE   0.012   0.001   PHE B 241 
 TRP   0.007   0.001   TRP B 339 
 HIS   0.004   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 6690)
  covalent geometry    : angle       0.43655 ( 9154)
  SS BOND              : bond        0.00038 (    1)
  SS BOND              : angle       0.28845 (    2)
  hydrogen bonds       : bond        0.03509 (  344)
  hydrogen bonds       : angle       3.69818 ( 1005)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.230 
Fit side-chains
REVERT: B  258 ASP cc_start: 0.8693 (t0) cc_final: 0.8342 (t0)
  outliers start: 8
  outliers final: 8
  residues processed: 77
  average time/residue: 0.0602
  time to fit residues: 6.9932
Evaluate side-chains
  80 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.123384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.103468 restraints weight = 9798.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 1.84
r_work: 0.3066 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8628
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6691  Z= 0.110
  Angle     :  0.444   6.790   9156  Z= 0.235
  Chirality :  0.040   0.142   1105
  Planarity :  0.003   0.036   1138
  Dihedral  :  6.154 117.739    975
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 13.41 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.72 (0.30), residues: 874
  helix:  2.75 (0.27), residues: 395
  sheet:  0.69 (0.43), residues: 157
  loop : -0.72 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 175 
 TYR   0.009   0.001   TYR B  59 
 PHE   0.012   0.001   PHE B 241 
 TRP   0.007   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 6690)
  covalent geometry    : angle       0.44421 ( 9154)
  SS BOND              : bond        0.00058 (    1)
  SS BOND              : angle       0.34405 (    2)
  hydrogen bonds       : bond        0.03681 (  344)
  hydrogen bonds       : angle       3.72466 ( 1005)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.209 
Fit side-chains
REVERT: B  258 ASP cc_start: 0.8743 (t0) cc_final: 0.8406 (t0)
  outliers start: 9
  outliers final: 9
  residues processed: 78
  average time/residue: 0.0535
  time to fit residues: 6.2860
Evaluate side-chains
  80 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0470
   chunk 9 optimal weight:    0.9980
   chunk 48 optimal weight:    0.1980
   chunk 82 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 71 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.124622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.104211 restraints weight = 9853.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 1.94
r_work: 0.3077 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6691  Z= 0.088
  Angle     :  0.427   6.603   9156  Z= 0.226
  Chirality :  0.039   0.131   1105
  Planarity :  0.002   0.036   1138
  Dihedral  :  5.995 115.038    975
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 14.07 %
    Favored  : 84.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.77 (0.30), residues: 874
  helix:  2.79 (0.27), residues: 395
  sheet:  0.73 (0.43), residues: 157
  loop : -0.70 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 175 
 TYR   0.008   0.001   TYR B  59 
 PHE   0.011   0.001   PHE B 241 
 TRP   0.007   0.001   TRP B 297 
 HIS   0.004   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00185 ( 6690)
  covalent geometry    : angle       0.42675 ( 9154)
  SS BOND              : bond        0.00007 (    1)
  SS BOND              : angle       0.16475 (    2)
  hydrogen bonds       : bond        0.03321 (  344)
  hydrogen bonds       : angle       3.66872 ( 1005)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1680.07 seconds
wall clock time: 29 minutes 23.53 seconds (1763.53 seconds total)