Starting phenix.real_space_refine
on Fri Aug 22 18:15:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gge_40004/08_2025/8gge_40004.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gge_40004/08_2025/8gge_40004.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gge_40004/08_2025/8gge_40004.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gge_40004/08_2025/8gge_40004.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gge_40004/08_2025/8gge_40004.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gge_40004/08_2025/8gge_40004.cif"
  }
  resolution = 3.5
  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=   0.019
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      32      5.16       5
     C    4236      2.51       5
     N    1204      2.21       5
     O    1233      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 6708
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2526
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 361, 2526
          Classifications: {'peptide': 361}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 133}
          Link IDs: {'PTRANS': 13, 'TRANS': 347}
          Chain breaks: 4
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 476
          Unresolved non-hydrogen angles: 592
          Unresolved non-hydrogen dihedrals: 378
          Unresolved non-hydrogen chiralities: 27
          Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 11, 'ASN:plan1': 8, 'GLU:plan': 23, 'ASP:plan': 19, 'PHE:plan': 5, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 304
    Chain: "B"
      Number of atoms: 2408
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2408
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 184
          Unresolved non-hydrogen angles: 226
          Unresolved non-hydrogen dihedrals: 142
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ASP:plan': 10, 'GLN:plan1': 6, 'ARG:plan': 9, 'GLU:plan': 8, 'ASN:plan1': 4}
          Unresolved non-hydrogen planarities: 143
    Chain: "G"
      Number of atoms: 340
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 340
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 66
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "R"
      Number of atoms: 1387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1387
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 142}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 7
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 505
          Unresolved non-hydrogen angles: 664
          Unresolved non-hydrogen dihedrals: 417
          Unresolved non-hydrogen chiralities: 67
          Planarities with less than four sites: {'TRP:plan': 4, 'PHE:plan': 9, 'ASN:plan1': 8, 'GLN:plan1': 7, 'TYR:plan': 6, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 5, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 252
    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: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.74, per 1000 atoms: 0.26
  Number of scatterers: 6708
  At special positions: 0
  Unit cell: (84.1669, 136.229, 103.256, 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      32     16.00
     P       3     15.00
     O    1233      8.00
     N    1204      7.00
     C    4236      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.54
  Conformation dependent library (CDL) restraints added in 342.9 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1870

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 8 sheets defined
      47.1% alpha, 13.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 3.938A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 64
      removed outlier: 3.704A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   VAL A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 113
      removed outlier: 3.600A  pdb=" N   GLU A 104 " --> pdb=" O   LYS A 100 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ILE A 106 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL A 107 " --> pdb=" O   ILE A 103 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   SER A 111 " --> pdb=" O   VAL A 107 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ASN A 112 " --> pdb=" O   ALA A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 136
      removed outlier: 4.135A  pdb=" N   TYR A 130 " --> pdb=" O   PHE A 126 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   SER A 133 " --> pdb=" O   ASP A 129 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ASN A 136 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 155
      removed outlier: 4.021A  pdb=" N   TYR A 147 " --> pdb=" O   PRO A 143 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   GLU A 148 " --> pdb=" O   PRO A 144 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   HIS A 149 " --> pdb=" O   GLU A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 164
    Processing helix  chain 'A' and resid 175 through 181
      removed outlier: 3.673A  pdb=" N   LYS A 181 " --> pdb=" O   TYR A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 187
    Processing helix  chain 'A' and resid 195 through 200
    Processing helix  chain 'A' and resid 232 through 237
      removed outlier: 3.995A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 4.069A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ALA A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.009A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.610A  pdb=" N   TYR A 339 " --> pdb=" O   THR A 335 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 389
      removed outlier: 3.843A  pdb=" N   ILE A 372 " --> pdb=" O   ASP A 368 " (cutoff:3.500A)
      removed outlier: 5.293A  pdb=" N   ASN A 377 " --> pdb=" O   ARG A 373 " (cutoff:3.500A)
      removed outlier: 5.665A  pdb=" N   ASP A 378 " --> pdb=" O   ARG A 374 " (cutoff:3.500A)
      removed outlier: 5.179A  pdb=" N   ILE A 383 " --> pdb=" O   CYS A 379 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   GLN A 384 " --> pdb=" O   ARG A 380 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   HIS A 387 " --> pdb=" O   ILE A 383 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ARG A 389 " --> pdb=" O   ARG A 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 26
      removed outlier: 4.054A  pdb=" N   GLN B   9 " --> pdb=" O   ASP B   5 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   GLU B  10 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.826A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 132
      removed outlier: 3.731A  pdb=" N   GLY B 131 " --> pdb=" O   THR B 128 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ASN B 132 " --> pdb=" O   ARG B 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 128 through 132'
    Processing helix  chain 'G' and resid 10 through 24
      removed outlier: 3.756A  pdb=" N   LYS G  14 " --> pdb=" O   ALA G  10 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLU G  17 " --> pdb=" O   ARG G  13 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.659A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 33 through 54
      removed outlier: 4.223A  pdb=" N   GLY R  37 " --> pdb=" O   VAL R  33 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU R  45 " --> pdb=" O   SER R  41 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ALA R  46 " --> pdb=" O   LEU R  42 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE R  47 " --> pdb=" O   ILE R  43 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 70 through 78
      removed outlier: 4.259A  pdb=" N   SER R  74 " --> pdb=" O   TYR R  70 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LEU R  75 " --> pdb=" O   PHE R  71 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 88 through 94
      removed outlier: 4.065A  pdb=" N   ALA R  92 " --> pdb=" O   PRO R  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.706A  pdb=" N   CYS R 106 " --> pdb=" O   GLY R 102 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   GLU R 107 " --> pdb=" O   ASN R 103 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   PHE R 108 " --> pdb=" O   PHE R 104 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ASP R 113 " --> pdb=" O   TRP R 109 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   SER R 137 " --> pdb=" O   PHE R 133 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 152 through 171
      removed outlier: 3.633A  pdb=" N   MET R 156 " --> pdb=" O   VAL R 152 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 198 through 208
    Processing helix  chain 'R' and resid 208 through 230
      removed outlier: 4.170A  pdb=" N   LEU R 212 " --> pdb=" O   PHE R 208 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   VAL R 216 " --> pdb=" O   LEU R 212 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   PHE R 217 " --> pdb=" O   VAL R 213 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   TYR R 219 " --> pdb=" O   MET R 215 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   SER R 220 " --> pdb=" O   VAL R 216 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   ARG R 221 " --> pdb=" O   PHE R 217 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   VAL R 222 " --> pdb=" O   VAL R 218 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LYS R 227 " --> pdb=" O   PHE R 223 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG R 228 " --> pdb=" O   GLN R 224 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 287
      removed outlier: 3.641A  pdb=" N   GLY R 276 " --> pdb=" O   LEU R 272 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   ILE R 277 " --> pdb=" O   LYS R 273 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 287 through 299
      removed outlier: 3.733A  pdb=" N   ILE R 291 " --> pdb=" O   LEU R 287 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   VAL R 295 " --> pdb=" O   ILE R 291 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 314
    Processing helix  chain 'R' and resid 317 through 326
      Proline residue:  R 323  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213
      removed outlier: 3.952A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 9.475A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.674A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.652A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 5.937A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.856A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   SER B  72 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE B  80 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE B  81 " --> pdb=" O   HIS B  91 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105
      removed outlier: 3.508A  pdb=" N   ALA B 113 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   SER B 122 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.265A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.902A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   SER B 160 " --> pdb=" O   CYS B 148 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 178 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.723A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.142A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.595A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU B 252 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.756A  pdb=" N   LEU B 285 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU B 308 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)

    312 hydrogen bonds defined for protein.
    909 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: 0.90

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1797
        1.33 -     1.45: 1256
        1.45 -     1.57: 3726
        1.57 -     1.69: 6
        1.69 -     1.81: 44
  Bond restraints: 6829
  Sorted by residual:
  bond pdb=" CA  GLN A 384 "
       pdb=" C   GLN A 384 "
    ideal  model  delta    sigma   weight residual
    1.524  1.442  0.082 1.32e-02 5.74e+03 3.86e+01
  bond pdb=" N   ARG A 385 "
       pdb=" CA  ARG A 385 "
    ideal  model  delta    sigma   weight residual
    1.459  1.408  0.051 1.19e-02 7.06e+03 1.85e+01
  bond pdb=" CA  PHE A 376 "
       pdb=" C   PHE A 376 "
    ideal  model  delta    sigma   weight residual
    1.526  1.474  0.052 1.39e-02 5.18e+03 1.40e+01
  bond pdb=" CA  LEU A 388 "
       pdb=" C   LEU A 388 "
    ideal  model  delta    sigma   weight residual
    1.523  1.475  0.048 1.30e-02 5.92e+03 1.38e+01
  bond pdb=" CA  ASP A 381 "
       pdb=" C   ASP A 381 "
    ideal  model  delta    sigma   weight residual
    1.527  1.481  0.046 1.30e-02 5.92e+03 1.26e+01
  ... (remaining 6824 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 9247
        2.17 -     4.35: 84
        4.35 -     6.52: 18
        6.52 -     8.69: 4
        8.69 -    10.87: 4
  Bond angle restraints: 9357
  Sorted by residual:
  angle pdb=" N   HIS A 387 "
        pdb=" CA  HIS A 387 "
        pdb=" C   HIS A 387 "
      ideal   model   delta    sigma   weight residual
     111.14  121.58  -10.44 1.08e+00 8.57e-01 9.34e+01
  angle pdb=" N   TYR A 391 "
        pdb=" CA  TYR A 391 "
        pdb=" C   TYR A 391 "
      ideal   model   delta    sigma   weight residual
     113.43  102.56   10.87 1.26e+00 6.30e-01 7.44e+01
  angle pdb=" N   ASP A 381 "
        pdb=" CA  ASP A 381 "
        pdb=" C   ASP A 381 "
      ideal   model   delta    sigma   weight residual
     111.39  102.62    8.77 1.38e+00 5.25e-01 4.04e+01
  angle pdb=" N   PHE A 376 "
        pdb=" CA  PHE A 376 "
        pdb=" C   PHE A 376 "
      ideal   model   delta    sigma   weight residual
     111.90  103.54    8.36 1.32e+00 5.74e-01 4.01e+01
  angle pdb=" N   CYS A 379 "
        pdb=" CA  CYS A 379 "
        pdb=" C   CYS A 379 "
      ideal   model   delta    sigma   weight residual
     111.52  102.69    8.83 1.40e+00 5.10e-01 3.98e+01
  ... (remaining 9352 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.57: 3667
       17.57 -    35.15: 239
       35.15 -    52.72: 41
       52.72 -    70.29: 4
       70.29 -    87.86: 3
  Dihedral angle restraints: 3954
    sinusoidal: 1088
      harmonic: 2866
  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   18.88   85.71     1      2.00e+01 2.50e-03 2.22e+01
  dihedral pdb=" CA  GLU A 259 "
           pdb=" C   GLU A 259 "
           pdb=" N   ASP A 260 "
           pdb=" CA  ASP A 260 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.32  -19.68     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CB  LYS B  89 "
           pdb=" CG  LYS B  89 "
           pdb=" CD  LYS B  89 "
           pdb=" CE  LYS B  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -109.82   49.82     3      1.50e+01 4.44e-03 8.82e+00
  ... (remaining 3951 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 916
       0.051 -    0.103: 176
       0.103 -    0.154: 34
       0.154 -    0.205: 2
       0.205 -    0.257: 1
  Chirality restraints: 1129
  Sorted by residual:
  chirality pdb=" CA  HIS A 387 "
            pdb=" N   HIS A 387 "
            pdb=" C   HIS A 387 "
            pdb=" CB  HIS A 387 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CA  GLU A 392 "
            pdb=" N   GLU A 392 "
            pdb=" C   GLU A 392 "
            pdb=" CB  GLU A 392 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.20e-01
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.56   -0.17 2.00e-01 2.50e+01 6.81e-01
  ... (remaining 1126 not shown)

  Planarity restraints: 1203
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 375 "   -0.011 2.00e-02 2.50e+03   2.16e-02 4.66e+00
        pdb=" C   VAL A 375 "    0.037 2.00e-02 2.50e+03
        pdb=" O   VAL A 375 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   PHE A 376 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 393 "   -0.010 2.00e-02 2.50e+03   2.03e-02 4.14e+00
        pdb=" C   LEU A 393 "    0.035 2.00e-02 2.50e+03
        pdb=" O   LEU A 393 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LEU A 394 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "    0.027 5.00e-02 4.00e+02   4.13e-02 2.73e+00
        pdb=" N   PRO G  49 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1200 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1249
        2.77 -     3.30: 6258
        3.30 -     3.83: 10166
        3.83 -     4.37: 10536
        4.37 -     4.90: 19574
  Nonbonded interactions: 47783
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" NZ  LYS A  53 "
            pdb=" O1G GTP A 401 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" O   VAL A 375 "
            pdb=" N   ASP A 378 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" O   MET R 171 "
            pdb=" ND1 HIS R 172 "
     model   vdw
     2.287 3.120
  ... (remaining 47778 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 group one per residue
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:             3.000
  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:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     7.130
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   6829  Z= 0.215
  Angle     :  0.593  10.867   9357  Z= 0.358
  Chirality :  0.042   0.257   1129
  Planarity :  0.003   0.041   1203
  Dihedral  : 12.439  87.864   2084
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  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: -0.02 (0.28), residues: 954
  helix:  1.70 (0.28), residues: 377
  sheet: -1.02 (0.40), residues: 184
  loop : -1.17 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  27 
 TYR   0.009   0.001   TYR R 174 
 PHE   0.021   0.001   PHE R 289 
 TRP   0.009   0.001   TRP R 286 
 HIS   0.006   0.001   HIS A 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 6829)
  covalent geometry    : angle       0.59281 ( 9357)
  hydrogen bonds       : bond        0.25487 (  312)
  hydrogen bonds       : angle       6.81229 (  909)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.256 
Fit side-chains
REVERT: A  331 ASP cc_start: 0.8236 (t0) cc_final: 0.7971 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.0594
  time to fit residues: 8.0238
Evaluate side-chains
  73 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0970
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    1.0180

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A 384 GLN
B  88 ASN
B 295 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.140082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.103263 restraints weight = 12092.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.106215 restraints weight = 6668.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.108133 restraints weight = 4723.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.109265 restraints weight = 3802.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.110202 restraints weight = 3337.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6829  Z= 0.135
  Angle     :  0.497   6.149   9357  Z= 0.274
  Chirality :  0.043   0.146   1129
  Planarity :  0.003   0.043   1203
  Dihedral  :  5.095  85.372   1059
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 12.18 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.07 (0.28), residues: 954
  helix:  1.64 (0.27), residues: 405
  sheet: -0.75 (0.41), residues: 180
  loop : -1.34 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  27 
 TYR   0.019   0.001   TYR R 174 
 PHE   0.020   0.002   PHE R 282 
 TRP   0.008   0.001   TRP R  99 
 HIS   0.007   0.001   HIS A 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6829)
  covalent geometry    : angle       0.49722 ( 9357)
  hydrogen bonds       : bond        0.04881 (  312)
  hydrogen bonds       : angle       4.65540 (  909)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A  154 TRP cc_start: 0.8053 (t-100) cc_final: 0.7262 (t-100)
REVERT: A  331 ASP cc_start: 0.7586 (t0) cc_final: 0.7341 (t70)
REVERT: A  368 ASP cc_start: 0.7959 (t0) cc_final: 0.7725 (t0)
  outliers start: 3
  outliers final: 2
  residues processed: 81
  average time/residue: 0.0454
  time to fit residues: 5.6053
Evaluate side-chains
  75 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 73
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  174 TYR
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 5 optimal weight:    0.2980
   chunk 10 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 96 optimal weight:    9.9990
   chunk 3 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 78 optimal weight:    0.0170
   overall best weight:    0.6222

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.141107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.104714 restraints weight = 11944.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.107539 restraints weight = 6775.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.109407 restraints weight = 4857.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.110626 restraints weight = 3949.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.111269 restraints weight = 3443.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6829  Z= 0.099
  Angle     :  0.447   6.242   9357  Z= 0.245
  Chirality :  0.041   0.153   1129
  Planarity :  0.003   0.040   1203
  Dihedral  :  4.896  83.996   1059
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 15.32 %
    Favored  : 83.69 %
  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:  0.27 (0.28), residues: 954
  helix:  1.79 (0.27), residues: 411
  sheet: -0.62 (0.40), residues: 184
  loop : -1.28 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  27 
 TYR   0.011   0.001   TYR R 174 
 PHE   0.021   0.001   PHE R 282 
 TRP   0.007   0.001   TRP R  99 
 HIS   0.006   0.001   HIS A 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 6829)
  covalent geometry    : angle       0.44721 ( 9357)
  hydrogen bonds       : bond        0.03790 (  312)
  hydrogen bonds       : angle       4.17965 (  909)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  154 TRP cc_start: 0.8028 (t-100) cc_final: 0.7237 (t-100)
REVERT: A  211 LYS cc_start: 0.8981 (mmtm) cc_final: 0.8660 (mmtt)
REVERT: A  331 ASP cc_start: 0.7475 (t0) cc_final: 0.7114 (t70)
REVERT: A  368 ASP cc_start: 0.7912 (t0) cc_final: 0.7492 (t0)
  outliers start: 5
  outliers final: 3
  residues processed: 85
  average time/residue: 0.0624
  time to fit residues: 7.8275
Evaluate side-chains
  76 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  376 PHE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 87 optimal weight:    0.0970
   chunk 34 optimal weight:    0.8980
   chunk 77 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 86 optimal weight:    4.9990
   chunk 55 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.3911 r_free = 0.3911 target = 0.141548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.104954 restraints weight = 12047.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.107834 restraints weight = 6657.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.109790 restraints weight = 4734.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.111030 restraints weight = 3806.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.111924 restraints weight = 3311.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6829  Z= 0.093
  Angle     :  0.433   6.267   9357  Z= 0.236
  Chirality :  0.041   0.155   1129
  Planarity :  0.003   0.041   1203
  Dihedral  :  4.769  83.011   1059
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 17.68 %
    Favored  : 80.55 %
  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:  0.46 (0.28), residues: 954
  helix:  2.02 (0.27), residues: 411
  sheet: -0.42 (0.41), residues: 178
  loop : -1.33 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  27 
 TYR   0.010   0.001   TYR A 130 
 PHE   0.023   0.001   PHE R 282 
 TRP   0.006   0.001   TRP R  99 
 HIS   0.006   0.001   HIS R 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00192 ( 6829)
  covalent geometry    : angle       0.43251 ( 9357)
  hydrogen bonds       : bond        0.03268 (  312)
  hydrogen bonds       : angle       3.86457 (  909)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A  154 TRP cc_start: 0.7950 (t-100) cc_final: 0.7150 (t-100)
REVERT: A  211 LYS cc_start: 0.8989 (mmtm) cc_final: 0.8617 (mmtm)
REVERT: A  331 ASP cc_start: 0.7357 (t0) cc_final: 0.6916 (t70)
REVERT: R  215 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6367 (mmm)
  outliers start: 9
  outliers final: 3
  residues processed: 85
  average time/residue: 0.0633
  time to fit residues: 8.0311
Evaluate side-chains
  76 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain R residue  215 MET
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 77 optimal weight:    3.9990
   chunk 75 optimal weight:   10.0000
   chunk 25 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9980
   chunk 88 optimal weight:    0.7980
   chunk 3 optimal weight:    0.2980
   chunk 40 optimal weight:    5.9990
   chunk 91 optimal weight:   10.0000
   chunk 55 optimal weight:    0.0030
   chunk 35 optimal weight:    0.0670
   overall best weight:    0.3928

-------------------------------------------------------------------------------
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 = 0.3923 r_free = 0.3923 target = 0.142561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.105942 restraints weight = 11993.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.108914 restraints weight = 6591.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.110929 restraints weight = 4638.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.112287 restraints weight = 3714.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.112953 restraints weight = 3208.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   6829  Z= 0.082
  Angle     :  0.424   6.911   9357  Z= 0.228
  Chirality :  0.040   0.151   1129
  Planarity :  0.003   0.040   1203
  Dihedral  :  4.605  81.694   1059
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 18.27 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.52 (0.28), residues: 954
  helix:  2.08 (0.27), residues: 412
  sheet: -0.52 (0.41), residues: 178
  loop : -1.26 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  27 
 TYR   0.010   0.001   TYR A 130 
 PHE   0.025   0.001   PHE R 282 
 TRP   0.006   0.001   TRP R  99 
 HIS   0.006   0.001   HIS R 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00158 ( 6829)
  covalent geometry    : angle       0.42410 ( 9357)
  hydrogen bonds       : bond        0.02861 (  312)
  hydrogen bonds       : angle       3.66009 (  909)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  154 TRP cc_start: 0.7878 (t-100) cc_final: 0.7078 (t-100)
REVERT: A  331 ASP cc_start: 0.7161 (t0) cc_final: 0.6781 (t70)
REVERT: A  352 SER cc_start: 0.7338 (m) cc_final: 0.7046 (t)
REVERT: R  215 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.6318 (mmm)
  outliers start: 8
  outliers final: 3
  residues processed: 87
  average time/residue: 0.0625
  time to fit residues: 7.8431
Evaluate side-chains
  78 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  215 MET
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 80 optimal weight:    0.0970
   chunk 40 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 27 optimal weight:    5.9990
   chunk 55 optimal weight:    0.8980
   chunk 36 optimal weight:   20.0000
   chunk 16 optimal weight:    6.9990
   overall best weight:    1.1380

-------------------------------------------------------------------------------
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 = 0.3891 r_free = 0.3891 target = 0.139861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.103284 restraints weight = 12063.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.106159 restraints weight = 6610.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.108031 restraints weight = 4700.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.109110 restraints weight = 3793.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.110109 restraints weight = 3323.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6829  Z= 0.128
  Angle     :  0.469   6.232   9357  Z= 0.255
  Chirality :  0.042   0.163   1129
  Planarity :  0.003   0.042   1203
  Dihedral  :  4.834  83.339   1059
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 19.45 %
    Favored  : 78.78 %
  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:  0.53 (0.29), residues: 954
  helix:  2.13 (0.27), residues: 410
  sheet: -0.48 (0.41), residues: 177
  loop : -1.30 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  27 
 TYR   0.008   0.001   TYR A 130 
 PHE   0.026   0.001   PHE R 282 
 TRP   0.006   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6829)
  covalent geometry    : angle       0.46912 ( 9357)
  hydrogen bonds       : bond        0.03496 (  312)
  hydrogen bonds       : angle       3.72356 (  909)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A  154 TRP cc_start: 0.7964 (t-100) cc_final: 0.7107 (t-100)
REVERT: A  331 ASP cc_start: 0.7330 (t0) cc_final: 0.6934 (t70)
REVERT: B  262 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7212 (mtt)
REVERT: R  215 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.6260 (mmm)
  outliers start: 9
  outliers final: 4
  residues processed: 80
  average time/residue: 0.0610
  time to fit residues: 7.2007
Evaluate side-chains
  80 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain R residue  215 MET
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 42 optimal weight:    0.4980
   chunk 93 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 68 optimal weight:    5.9990
   chunk 36 optimal weight:   20.0000
   chunk 33 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 8 optimal weight:    8.9990
   chunk 89 optimal weight:    0.3980
   chunk 24 optimal weight:    0.9990
   chunk 72 optimal weight:    0.0370
   overall best weight:    0.5862

-------------------------------------------------------------------------------
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 = 0.3911 r_free = 0.3911 target = 0.141520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.105010 restraints weight = 11926.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.107876 restraints weight = 6616.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.109859 restraints weight = 4684.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.110926 restraints weight = 3768.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.111922 restraints weight = 3301.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6829  Z= 0.090
  Angle     :  0.438   6.236   9357  Z= 0.236
  Chirality :  0.041   0.136   1129
  Planarity :  0.003   0.038   1203
  Dihedral  :  4.707  82.207   1059
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 20.04 %
    Favored  : 78.78 %
  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:  0.62 (0.29), residues: 954
  helix:  2.14 (0.27), residues: 411
  sheet: -0.26 (0.42), residues: 174
  loop : -1.29 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  27 
 TYR   0.009   0.001   TYR A 130 
 PHE   0.028   0.001   PHE R 282 
 TRP   0.005   0.001   TRP R  99 
 HIS   0.007   0.001   HIS R 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00189 ( 6829)
  covalent geometry    : angle       0.43818 ( 9357)
  hydrogen bonds       : bond        0.02980 (  312)
  hydrogen bonds       : angle       3.60398 (  909)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  154 TRP cc_start: 0.7901 (t-100) cc_final: 0.7043 (t-100)
REVERT: A  331 ASP cc_start: 0.7260 (t0) cc_final: 0.6864 (t70)
REVERT: B  262 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.7257 (mtt)
REVERT: B  292 PHE cc_start: 0.8792 (m-80) cc_final: 0.8299 (m-80)
REVERT: R  215 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6221 (mmm)
  outliers start: 6
  outliers final: 4
  residues processed: 82
  average time/residue: 0.0560
  time to fit residues: 6.8270
Evaluate side-chains
  81 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain R residue  215 MET
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 68 optimal weight:    4.9990
   chunk 49 optimal weight:    0.2980
   chunk 51 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.139722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.103354 restraints weight = 12084.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.106216 restraints weight = 6677.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.108120 restraints weight = 4733.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.109260 restraints weight = 3823.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.110101 restraints weight = 3342.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6829  Z= 0.122
  Angle     :  0.461   6.238   9357  Z= 0.250
  Chirality :  0.041   0.143   1129
  Planarity :  0.003   0.042   1203
  Dihedral  :  4.867  83.144   1059
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 20.24 %
    Favored  : 78.19 %
  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:  0.59 (0.29), residues: 954
  helix:  2.17 (0.27), residues: 410
  sheet: -0.41 (0.42), residues: 177
  loop : -1.28 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  27 
 TYR   0.007   0.001   TYR A 130 
 PHE   0.028   0.001   PHE R 282 
 TRP   0.006   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6829)
  covalent geometry    : angle       0.46119 ( 9357)
  hydrogen bonds       : bond        0.03425 (  312)
  hydrogen bonds       : angle       3.66230 (  909)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A  154 TRP cc_start: 0.7937 (t-100) cc_final: 0.7065 (t-100)
REVERT: A  211 LYS cc_start: 0.9116 (mptt) cc_final: 0.8893 (mmtt)
REVERT: A  331 ASP cc_start: 0.7365 (t0) cc_final: 0.7045 (t70)
REVERT: R  215 MET cc_start: 0.6803 (OUTLIER) cc_final: 0.6087 (mmm)
  outliers start: 8
  outliers final: 5
  residues processed: 80
  average time/residue: 0.0619
  time to fit residues: 7.3285
Evaluate side-chains
  80 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain R residue  215 MET
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 62 optimal weight:    5.9990
   chunk 92 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 75 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 88 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0170
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.141454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.104739 restraints weight = 11958.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.107662 restraints weight = 6536.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.109643 restraints weight = 4621.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.110950 restraints weight = 3699.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.111626 restraints weight = 3199.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6829  Z= 0.090
  Angle     :  0.442   6.243   9357  Z= 0.238
  Chirality :  0.041   0.140   1129
  Planarity :  0.003   0.040   1203
  Dihedral  :  4.745  82.220   1059
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 21.02 %
    Favored  : 77.80 %
  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:  0.62 (0.29), residues: 954
  helix:  2.23 (0.27), residues: 410
  sheet: -0.33 (0.42), residues: 176
  loop : -1.34 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  27 
 TYR   0.009   0.001   TYR A 130 
 PHE   0.027   0.001   PHE R 282 
 TRP   0.005   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00189 ( 6829)
  covalent geometry    : angle       0.44231 ( 9357)
  hydrogen bonds       : bond        0.03016 (  312)
  hydrogen bonds       : angle       3.55565 (  909)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  154 TRP cc_start: 0.7930 (t-100) cc_final: 0.7081 (t-100)
REVERT: A  211 LYS cc_start: 0.9103 (mptt) cc_final: 0.8893 (mmtt)
REVERT: A  331 ASP cc_start: 0.7179 (t0) cc_final: 0.6894 (t70)
REVERT: R  215 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.5996 (mmm)
  outliers start: 6
  outliers final: 5
  residues processed: 83
  average time/residue: 0.0618
  time to fit residues: 7.6334
Evaluate side-chains
  84 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  215 MET
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 78 optimal weight:   20.0000
   chunk 54 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 34 optimal weight:    7.9990
   chunk 76 optimal weight:   20.0000
   chunk 16 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9980
   chunk 74 optimal weight:    9.9990
   chunk 35 optimal weight:    0.7980
   chunk 83 optimal weight:   20.0000
   chunk 31 optimal weight:    0.8980
   overall best weight:    1.5382

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.138761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.102370 restraints weight = 12063.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.105166 restraints weight = 6697.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.107018 restraints weight = 4760.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.108283 restraints weight = 3853.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.108946 restraints weight = 3348.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6829  Z= 0.162
  Angle     :  0.510   7.270   9357  Z= 0.275
  Chirality :  0.043   0.170   1129
  Planarity :  0.003   0.041   1203
  Dihedral  :  5.019  83.447   1059
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 20.43 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.53 (0.29), residues: 954
  helix:  2.14 (0.27), residues: 410
  sheet: -0.43 (0.42), residues: 175
  loop : -1.35 (0.31), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  27 
 TYR   0.008   0.001   TYR B 145 
 PHE   0.028   0.002   PHE R 282 
 TRP   0.007   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 6829)
  covalent geometry    : angle       0.51049 ( 9357)
  hydrogen bonds       : bond        0.03737 (  312)
  hydrogen bonds       : angle       3.71785 (  909)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A  331 ASP cc_start: 0.7336 (t0) cc_final: 0.7000 (t70)
REVERT: A  368 ASP cc_start: 0.7896 (t70) cc_final: 0.7103 (t0)
REVERT: R  215 MET cc_start: 0.6798 (OUTLIER) cc_final: 0.6092 (mmm)
  outliers start: 8
  outliers final: 7
  residues processed: 79
  average time/residue: 0.0645
  time to fit residues: 7.5406
Evaluate side-chains
  78 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain R residue  215 MET
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 36 optimal weight:   20.0000
   chunk 17 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 76 optimal weight:    0.0970
   chunk 33 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
B 142 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.140025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.103413 restraints weight = 11997.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.106309 restraints weight = 6572.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.108276 restraints weight = 4644.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.109513 restraints weight = 3733.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.110409 restraints weight = 3244.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6829  Z= 0.107
  Angle     :  0.462   6.201   9357  Z= 0.251
  Chirality :  0.041   0.174   1129
  Planarity :  0.003   0.039   1203
  Dihedral  :  4.916  83.030   1059
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 21.02 %
    Favored  : 77.60 %
  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:  0.56 (0.29), residues: 954
  helix:  2.19 (0.27), residues: 410
  sheet: -0.38 (0.42), residues: 175
  loop : -1.39 (0.31), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  27 
 TYR   0.008   0.001   TYR R 174 
 PHE   0.027   0.001   PHE R 282 
 TRP   0.006   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 6829)
  covalent geometry    : angle       0.46168 ( 9357)
  hydrogen bonds       : bond        0.03313 (  312)
  hydrogen bonds       : angle       3.63668 (  909)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1417.65 seconds
wall clock time: 24 minutes 59.64 seconds (1499.64 seconds total)