Starting phenix.real_space_refine
on Wed Mar  4 07:30:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wr4_21876/03_2026/6wr4_21876.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wr4_21876/03_2026/6wr4_21876.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wr4_21876/03_2026/6wr4_21876.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wr4_21876/03_2026/6wr4_21876.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wr4_21876/03_2026/6wr4_21876.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wr4_21876/03_2026/6wr4_21876.map"
  }
  resolution = 2.9
  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=   0.009 sd=   0.160
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    7896      2.51       5
     N    1941      2.21       5
     O    2037      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11934
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 470, 3862
          Classifications: {'peptide': 470}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 452}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "A"
      Number of atoms: 116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 116
          Unusual residues: {'LMN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 10
  Restraints were copied for chains:
    B, C
  Residues with excluded nonbonded symmetry interactions: 6
    residue:
      pdb=" C1  LMN A 901 " occ=0.50
      ... (67 atoms not shown)
      pdb=" OCB LMN A 901 " occ=0.50
    residue:
      pdb=" C1  LMN A 902 " occ=0.50
      ... (45 atoms not shown)
      pdb=" OBY LMN A 902 " occ=0.50
    residue:
      pdb=" C1  LMN B 901 " occ=0.50
      ... (67 atoms not shown)
      pdb=" OCB LMN B 901 " occ=0.50
    residue:
      pdb=" C1  LMN B 902 " occ=0.50
      ... (45 atoms not shown)
      pdb=" OBY LMN B 902 " occ=0.50
    residue:
      pdb=" C1  LMN C 901 " occ=0.50
      ... (67 atoms not shown)
      pdb=" OCB LMN C 901 " occ=0.50
    residue:
      pdb=" C1  LMN C 902 " occ=0.50
      ... (45 atoms not shown)
      pdb=" OBY LMN C 902 " occ=0.50
  Time building chain proxies: 3.15, per 1000 atoms: 0.26
  Number of scatterers: 11934
  At special positions: 0
  Unit cell: (132.5, 124.02, 85.86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    2037      8.00
     N    1941      7.00
     C    7896      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: 0.92
  Conformation dependent library (CDL) restraints added in 471.1 milliseconds
  

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2688

  Finding SS restraints...
    Secondary structure from input PDB file:
      75 helices and 6 sheets defined
      69.8% alpha, 2.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 42 through 56
      removed outlier: 3.671A  pdb=" N   PHE A  47 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 86
      removed outlier: 3.649A  pdb=" N   PHE A  68 " --> pdb=" O   ILE A  64 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLU A  69 " --> pdb=" O   GLY A  65 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU A  70 " --> pdb=" O   GLU A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 94
      removed outlier: 3.530A  pdb=" N   LEU A  92 " --> pdb=" O   ASP A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 115
    Processing helix  chain 'A' and resid 118 through 123
    Processing helix  chain 'A' and resid 129 through 167
      removed outlier: 3.886A  pdb=" N   GLU A 159 " --> pdb=" O   CYS A 155 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ILE A 160 " --> pdb=" O   CYS A 156 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   PHE A 163 " --> pdb=" O   GLU A 159 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU A 165 " --> pdb=" O   HIS A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 190
      removed outlier: 3.532A  pdb=" N   ALA A 185 " --> pdb=" O   GLN A 181 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   GLN A 189 " --> pdb=" O   ALA A 185 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   THR A 190 " --> pdb=" O   ARG A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 213
    Processing helix  chain 'A' and resid 215 through 225
      removed outlier: 4.044A  pdb=" N   MET A 219 " --> pdb=" O   PHE A 215 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ALA A 221 " --> pdb=" O   ASN A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 256
      removed outlier: 3.821A  pdb=" N   ASN A 250 " --> pdb=" O   GLY A 246 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLU A 252 " --> pdb=" O   LYS A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 275
      removed outlier: 3.554A  pdb=" N   LYS A 274 " --> pdb=" O   ALA A 271 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ARG A 275 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 271 through 275'
    Processing helix  chain 'A' and resid 279 through 300
      removed outlier: 3.830A  pdb=" N   LEU A 286 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   LEU A 291 " --> pdb=" O   SER A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 323
      removed outlier: 3.569A  pdb=" N   TRP A 307 " --> pdb=" O   LEU A 303 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ALA A 317 " --> pdb=" O   PHE A 313 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   GLU A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
      removed outlier: 5.750A  pdb=" N   VAL A 319 " --> pdb=" O   SER A 315 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   LYS A 321 " --> pdb=" O   ALA A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 340
    Processing helix  chain 'A' and resid 346 through 355
      removed outlier: 3.580A  pdb=" N   GLN A 351 " --> pdb=" O   GLU A 347 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ARG A 353 " --> pdb=" O   GLU A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 365
      removed outlier: 3.820A  pdb=" N   LYS A 363 " --> pdb=" O   LYS A 359 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   MET A 365 " --> pdb=" O   ALA A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 369
      removed outlier: 4.030A  pdb=" N   LEU A 369 " --> pdb=" O   ASN A 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 366 through 369'
    Processing helix  chain 'A' and resid 370 through 399
      removed outlier: 3.541A  pdb=" N   PHE A 383 " --> pdb=" O   ASN A 379 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ILE A 387 " --> pdb=" O   PHE A 383 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ASP A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 425
    Processing helix  chain 'A' and resid 437 through 445
      removed outlier: 3.751A  pdb=" N   ALA A 443 " --> pdb=" O   ARG A 439 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   HIS A 444 " --> pdb=" O   VAL A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 469
      removed outlier: 3.942A  pdb=" N   LEU A 468 " --> pdb=" O   GLU A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 481
      removed outlier: 3.603A  pdb=" N   PHE A 475 " --> pdb=" O   TYR A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 492
      Proline residue:  A 487  - end of helix
    Processing helix  chain 'A' and resid 494 through 496
      No H-bonds generated for 'chain 'A' and resid 494 through 496'
    Processing helix  chain 'A' and resid 497 through 508
    Processing helix  chain 'B' and resid 42 through 56
      removed outlier: 3.671A  pdb=" N   PHE B  47 " --> pdb=" O   LEU B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 86
      removed outlier: 3.649A  pdb=" N   PHE B  68 " --> pdb=" O   ILE B  64 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLU B  69 " --> pdb=" O   GLY B  65 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU B  70 " --> pdb=" O   GLU B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 94
      removed outlier: 3.529A  pdb=" N   LEU B  92 " --> pdb=" O   ASP B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 115
    Processing helix  chain 'B' and resid 118 through 123
    Processing helix  chain 'B' and resid 129 through 167
      removed outlier: 3.886A  pdb=" N   GLU B 159 " --> pdb=" O   CYS B 155 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ILE B 160 " --> pdb=" O   CYS B 156 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   PHE B 163 " --> pdb=" O   GLU B 159 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU B 165 " --> pdb=" O   HIS B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 190
      removed outlier: 3.531A  pdb=" N   ALA B 185 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   GLN B 189 " --> pdb=" O   ALA B 185 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   THR B 190 " --> pdb=" O   ARG B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 213
    Processing helix  chain 'B' and resid 215 through 225
      removed outlier: 4.043A  pdb=" N   MET B 219 " --> pdb=" O   PHE B 215 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ALA B 221 " --> pdb=" O   ASN B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 256
      removed outlier: 3.821A  pdb=" N   ASN B 250 " --> pdb=" O   GLY B 246 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLU B 252 " --> pdb=" O   LYS B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 275
      removed outlier: 3.555A  pdb=" N   LYS B 274 " --> pdb=" O   ALA B 271 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ARG B 275 " --> pdb=" O   GLU B 272 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 271 through 275'
    Processing helix  chain 'B' and resid 279 through 300
      removed outlier: 3.831A  pdb=" N   LEU B 286 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   LEU B 291 " --> pdb=" O   SER B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 323
      removed outlier: 3.568A  pdb=" N   TRP B 307 " --> pdb=" O   LEU B 303 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ALA B 317 " --> pdb=" O   PHE B 313 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   GLU B 318 " --> pdb=" O   PHE B 314 " (cutoff:3.500A)
      removed outlier: 5.750A  pdb=" N   VAL B 319 " --> pdb=" O   SER B 315 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   LYS B 321 " --> pdb=" O   ALA B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 333 through 340
    Processing helix  chain 'B' and resid 346 through 355
      removed outlier: 3.580A  pdb=" N   GLN B 351 " --> pdb=" O   GLU B 347 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ARG B 353 " --> pdb=" O   GLU B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 365
      removed outlier: 3.820A  pdb=" N   LYS B 363 " --> pdb=" O   LYS B 359 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   MET B 365 " --> pdb=" O   ALA B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 369
      removed outlier: 4.031A  pdb=" N   LEU B 369 " --> pdb=" O   ASN B 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 366 through 369'
    Processing helix  chain 'B' and resid 370 through 399
      removed outlier: 3.541A  pdb=" N   PHE B 383 " --> pdb=" O   ASN B 379 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ILE B 387 " --> pdb=" O   PHE B 383 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ASP B 398 " --> pdb=" O   LEU B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 425
    Processing helix  chain 'B' and resid 437 through 445
      removed outlier: 3.752A  pdb=" N   ALA B 443 " --> pdb=" O   ARG B 439 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   HIS B 444 " --> pdb=" O   VAL B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 464 through 469
      removed outlier: 3.942A  pdb=" N   LEU B 468 " --> pdb=" O   GLU B 464 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 471 through 481
      removed outlier: 3.603A  pdb=" N   PHE B 475 " --> pdb=" O   TYR B 471 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 481 through 492
      Proline residue:  B 487  - end of helix
    Processing helix  chain 'B' and resid 494 through 496
      No H-bonds generated for 'chain 'B' and resid 494 through 496'
    Processing helix  chain 'B' and resid 497 through 508
    Processing helix  chain 'C' and resid 42 through 56
      removed outlier: 3.671A  pdb=" N   PHE C  47 " --> pdb=" O   LEU C  43 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 58 through 86
      removed outlier: 3.650A  pdb=" N   PHE C  68 " --> pdb=" O   ILE C  64 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLU C  69 " --> pdb=" O   GLY C  65 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU C  70 " --> pdb=" O   GLU C  66 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 88 through 94
      removed outlier: 3.528A  pdb=" N   LEU C  92 " --> pdb=" O   ASP C  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 115
    Processing helix  chain 'C' and resid 118 through 123
    Processing helix  chain 'C' and resid 129 through 167
      removed outlier: 3.887A  pdb=" N   GLU C 159 " --> pdb=" O   CYS C 155 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ILE C 160 " --> pdb=" O   CYS C 156 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   PHE C 163 " --> pdb=" O   GLU C 159 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LEU C 165 " --> pdb=" O   HIS C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 190
      removed outlier: 3.531A  pdb=" N   ALA C 185 " --> pdb=" O   GLN C 181 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLN C 189 " --> pdb=" O   ALA C 185 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   THR C 190 " --> pdb=" O   ARG C 186 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 213
    Processing helix  chain 'C' and resid 215 through 225
      removed outlier: 4.043A  pdb=" N   MET C 219 " --> pdb=" O   PHE C 215 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ALA C 221 " --> pdb=" O   ASN C 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 244 through 256
      removed outlier: 3.822A  pdb=" N   ASN C 250 " --> pdb=" O   GLY C 246 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLU C 252 " --> pdb=" O   LYS C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 271 through 275
      removed outlier: 3.554A  pdb=" N   LYS C 274 " --> pdb=" O   ALA C 271 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ARG C 275 " --> pdb=" O   GLU C 272 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 271 through 275'
    Processing helix  chain 'C' and resid 279 through 300
      removed outlier: 3.831A  pdb=" N   LEU C 286 " --> pdb=" O   LEU C 282 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   LEU C 291 " --> pdb=" O   SER C 287 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 300 through 323
      removed outlier: 3.568A  pdb=" N   TRP C 307 " --> pdb=" O   LEU C 303 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ALA C 317 " --> pdb=" O   PHE C 313 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   GLU C 318 " --> pdb=" O   PHE C 314 " (cutoff:3.500A)
      removed outlier: 5.749A  pdb=" N   VAL C 319 " --> pdb=" O   SER C 315 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   LYS C 321 " --> pdb=" O   ALA C 317 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 333 through 340
    Processing helix  chain 'C' and resid 346 through 355
      removed outlier: 3.580A  pdb=" N   GLN C 351 " --> pdb=" O   GLU C 347 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ARG C 353 " --> pdb=" O   GLU C 349 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 357 through 365
      removed outlier: 3.819A  pdb=" N   LYS C 363 " --> pdb=" O   LYS C 359 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   MET C 365 " --> pdb=" O   ALA C 361 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 366 through 369
      removed outlier: 4.029A  pdb=" N   LEU C 369 " --> pdb=" O   ASN C 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 366 through 369'
    Processing helix  chain 'C' and resid 370 through 399
      removed outlier: 3.541A  pdb=" N   PHE C 383 " --> pdb=" O   ASN C 379 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ILE C 387 " --> pdb=" O   PHE C 383 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ASP C 398 " --> pdb=" O   LEU C 394 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 425
    Processing helix  chain 'C' and resid 437 through 445
      removed outlier: 3.752A  pdb=" N   ALA C 443 " --> pdb=" O   ARG C 439 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   HIS C 444 " --> pdb=" O   VAL C 440 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 464 through 469
      removed outlier: 3.942A  pdb=" N   LEU C 468 " --> pdb=" O   GLU C 464 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 471 through 481
      removed outlier: 3.603A  pdb=" N   PHE C 475 " --> pdb=" O   TYR C 471 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 481 through 492
      Proline residue:  C 487  - end of helix
    Processing helix  chain 'C' and resid 494 through 496
      No H-bonds generated for 'chain 'C' and resid 494 through 496'
    Processing helix  chain 'C' and resid 497 through 508
    Processing sheet with id=AA1, first strand: chain 'A' and resid 231 through 234
      removed outlier: 3.532A  pdb=" N   GLY A 238 " --> pdb=" O   LEU A 234 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 510 through 512
    Processing sheet with id=AA3, first strand: chain 'B' and resid 231 through 234
      removed outlier: 3.533A  pdb=" N   GLY B 238 " --> pdb=" O   LEU B 234 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 510 through 512
    Processing sheet with id=AA5, first strand: chain 'C' and resid 231 through 234
      removed outlier: 3.532A  pdb=" N   GLY C 238 " --> pdb=" O   LEU C 234 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 510 through 512

    597 hydrogen bonds defined for protein.
    1755 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.79

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3471
        1.34 -     1.46: 2483
        1.46 -     1.58: 6173
        1.58 -     1.69: 62
        1.69 -     1.81: 78
  Bond restraints: 12267
  Sorted by residual:
  bond pdb=" C1  LMN A 902 "
       pdb=" O5  LMN A 902 "
    ideal  model  delta    sigma   weight residual
    1.403  1.562 -0.159 2.00e-02 2.50e+03 6.35e+01
  bond pdb=" C1  LMN C 902 "
       pdb=" O5  LMN C 902 "
    ideal  model  delta    sigma   weight residual
    1.403  1.562 -0.159 2.00e-02 2.50e+03 6.33e+01
  bond pdb=" C1  LMN B 902 "
       pdb=" O5  LMN B 902 "
    ideal  model  delta    sigma   weight residual
    1.403  1.561 -0.158 2.00e-02 2.50e+03 6.28e+01
  bond pdb=" C1  LMN A 901 "
       pdb=" O5  LMN A 901 "
    ideal  model  delta    sigma   weight residual
    1.403  1.551 -0.148 2.00e-02 2.50e+03 5.49e+01
  bond pdb=" C1  LMN C 901 "
       pdb=" O5  LMN C 901 "
    ideal  model  delta    sigma   weight residual
    1.403  1.551 -0.148 2.00e-02 2.50e+03 5.48e+01
  ... (remaining 12262 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 15152
        2.19 -     4.38: 1166
        4.38 -     6.57: 245
        6.57 -     8.76: 75
        8.76 -    10.96: 18
  Bond angle restraints: 16656
  Sorted by residual:
  angle pdb=" N   THR C 461 "
        pdb=" CA  THR C 461 "
        pdb=" C   THR C 461 "
      ideal   model   delta    sigma   weight residual
     114.75  106.70    8.05 1.26e+00 6.30e-01 4.08e+01
  angle pdb=" N   THR B 461 "
        pdb=" CA  THR B 461 "
        pdb=" C   THR B 461 "
      ideal   model   delta    sigma   weight residual
     114.75  106.72    8.03 1.26e+00 6.30e-01 4.07e+01
  angle pdb=" N   THR A 461 "
        pdb=" CA  THR A 461 "
        pdb=" C   THR A 461 "
      ideal   model   delta    sigma   weight residual
     114.75  106.75    8.00 1.26e+00 6.30e-01 4.03e+01
  angle pdb=" C   LEU A 203 "
        pdb=" N   THR A 204 "
        pdb=" CA  THR A 204 "
      ideal   model   delta    sigma   weight residual
     121.54  131.51   -9.97 1.91e+00 2.74e-01 2.73e+01
  angle pdb=" C   LEU C 203 "
        pdb=" N   THR C 204 "
        pdb=" CA  THR C 204 "
      ideal   model   delta    sigma   weight residual
     121.54  131.45   -9.91 1.91e+00 2.74e-01 2.69e+01
  ... (remaining 16651 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.18: 6954
       24.18 -    48.36: 387
       48.36 -    72.54: 84
       72.54 -    96.72: 57
       96.72 -   120.90: 51
  Dihedral angle restraints: 7533
    sinusoidal: 3387
      harmonic: 4146
  Sorted by residual:
  dihedral pdb=" CA  PRO B  36 "
           pdb=" C   PRO B  36 "
           pdb=" N   TRP B  37 "
           pdb=" CA  TRP B  37 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.41  -41.59     0      5.00e+00 4.00e-02 6.92e+01
  dihedral pdb=" CA  PRO C  36 "
           pdb=" C   PRO C  36 "
           pdb=" N   TRP C  37 "
           pdb=" CA  TRP C  37 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.42  -41.58     0      5.00e+00 4.00e-02 6.91e+01
  dihedral pdb=" CA  GLN C 436 "
           pdb=" C   GLN C 436 "
           pdb=" N   LEU C 437 "
           pdb=" CA  LEU C 437 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  138.43   41.57     0      5.00e+00 4.00e-02 6.91e+01
  ... (remaining 7530 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 1658
       0.096 -    0.191: 223
       0.191 -    0.287: 12
       0.287 -    0.382: 12
       0.382 -    0.478: 3
  Chirality restraints: 1908
  Sorted by residual:
  chirality pdb=" CA  ARG C 279 "
            pdb=" N   ARG C 279 "
            pdb=" C   ARG C 279 "
            pdb=" CB  ARG C 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.71e+00
  chirality pdb=" CA  ARG B 279 "
            pdb=" N   ARG B 279 "
            pdb=" C   ARG B 279 "
            pdb=" CB  ARG B 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.68e+00
  chirality pdb=" CA  ARG A 279 "
            pdb=" N   ARG A 279 "
            pdb=" C   ARG A 279 "
            pdb=" CB  ARG A 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.65e+00
  ... (remaining 1905 not shown)

  Planarity restraints: 2013
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET C 448 "   -0.043 5.00e-02 4.00e+02   6.51e-02 6.78e+00
        pdb=" N   PRO C 449 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO C 449 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO C 449 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 448 "   -0.043 5.00e-02 4.00e+02   6.48e-02 6.72e+00
        pdb=" N   PRO B 449 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO B 449 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 449 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 448 "    0.043 5.00e-02 4.00e+02   6.48e-02 6.71e+00
        pdb=" N   PRO A 449 "   -0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO A 449 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 449 "    0.035 5.00e-02 4.00e+02
  ... (remaining 2010 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 3124
        2.80 -     3.32: 10383
        3.32 -     3.85: 19091
        3.85 -     4.37: 23463
        4.37 -     4.90: 38289
  Nonbonded interactions: 94350
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 261 "
            pdb=" O   LEU B 262 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OG  SER C 261 "
            pdb=" O   LEU C 262 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OG  SER A 261 "
            pdb=" O   LEU A 262 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   ILE C 254 "
            pdb=" NH1 ARG C 289 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" O   ILE B 254 "
            pdb=" NH1 ARG B 289 "
     model   vdw
     2.298 3.120
  ... (remaining 94345 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     11.830
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6888
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      :  0.012   0.159  12267  Z= 0.558
  Angle     :  1.398  10.956  16656  Z= 0.735
  Chirality :  0.070   0.478   1908
  Planarity :  0.007   0.065   2013
  Dihedral  : 20.663 120.896   4845
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  5.17 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  :  2.64 %
    Favored  : 91.83 %
  Cbeta Deviations :  0.22 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.89 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -6.12 (0.14), residues: 1392
  helix: -4.16 (0.08), residues: 921
  sheet:  None (None), residues: 0
  loop : -3.37 (0.22), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.027   0.002   ARG A 214 
 TYR   0.020   0.003   TYR B 218 
 PHE   0.034   0.003   PHE A 243 
 TRP   0.022   0.003   TRP A 257 
 HIS   0.011   0.002   HIS C 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.01174 (12267)
  covalent geometry    : angle       1.39823 (16656)
  hydrogen bonds       : bond        0.30275 (  597)
  hydrogen bonds       : angle      10.16717 ( 1755)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 252
  time to evaluate  : 0.457 
Fit side-chains
REVERT: A  172 MET cc_start: 0.6909 (mmp) cc_final: 0.6696 (mmt)
REVERT: A  245 ARG cc_start: 0.7000 (ttt-90) cc_final: 0.6784 (ttt180)
REVERT: A  448 MET cc_start: 0.6421 (mmt) cc_final: 0.5882 (mmt)
REVERT: B  504 PHE cc_start: 0.7359 (t80) cc_final: 0.7081 (t80)
REVERT: C  245 ARG cc_start: 0.6834 (ttt-90) cc_final: 0.6544 (ttt180)
  outliers start: 69
  outliers final: 4
  residues processed: 312
  average time/residue: 0.5376
  time to fit residues: 182.3658
Evaluate side-chains
  153 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 149
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 ASN
Chi-restraints excluded: chain A residue  399 GLU
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain B residue  288 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.3980
   chunk 55 optimal weight:    6.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 191 GLN
A 217 ASN
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 278 GLN
A 348 HIS
A 428 GLN
A 451 HIS
A 457 HIS
B 191 GLN
B 217 ASN
** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 278 GLN
B 348 HIS
** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 451 HIS
B 455 ASN
B 457 HIS
C  57 ASN
C 191 GLN
C 217 ASN
** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 278 GLN
C 348 HIS
** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 451 HIS
C 457 HIS

Total number of N/Q/H flips: 21

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.185823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.158232 restraints weight = 13472.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3762 rms_B_bonded: 2.16
r_work: 0.3538 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3528
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3528 r_free = 0.3528    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3527 r_free = 0.3527    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3527
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12267  Z= 0.163
  Angle     :  0.807   8.267  16656  Z= 0.398
  Chirality :  0.047   0.203   1908
  Planarity :  0.006   0.060   2013
  Dihedral  : 18.297 105.235   2153
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 10.34 %
    Favored  : 86.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.67 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.49 (0.19), residues: 1392
  helix: -1.77 (0.15), residues: 939
  sheet: -4.48 (0.57), residues: 30
  loop : -3.08 (0.24), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 289 
 TYR   0.016   0.001   TYR A 177 
 PHE   0.013   0.001   PHE A  79 
 TRP   0.015   0.001   TRP C 180 
 HIS   0.005   0.001   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (12267)
  covalent geometry    : angle       0.80745 (16656)
  hydrogen bonds       : bond        0.05372 (  597)
  hydrogen bonds       : angle       4.90392 ( 1755)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 175
  time to evaluate  : 0.457 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.7982 (mt) cc_final: 0.7677 (tp)
REVERT: A  292 TRP cc_start: 0.6846 (m100) cc_final: 0.6409 (m-10)
REVERT: B  292 TRP cc_start: 0.7111 (m100) cc_final: 0.6674 (m-10)
REVERT: C  292 TRP cc_start: 0.6955 (m100) cc_final: 0.6509 (m-10)
  outliers start: 36
  outliers final: 11
  residues processed: 198
  average time/residue: 0.5135
  time to fit residues: 111.2645
Evaluate side-chains
  136 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 125
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 PRO
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain B residue   36 PRO
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain C residue   36 PRO
Chi-restraints excluded: chain C residue  145 HIS
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  340 LEU
Chi-restraints excluded: chain C residue  489 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 120 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0570
   chunk 140 optimal weight:   10.0000
   chunk 86 optimal weight:    6.9990
   chunk 96 optimal weight:    8.9990
   chunk 19 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 121 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 32 optimal weight:   10.0000
   overall best weight:    1.5904

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 250 ASN
A 351 GLN
A 455 ASN
B  57 ASN
** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 250 ASN
B 351 GLN
B 406 HIS
C 250 ASN
C 351 GLN
** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.180804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.153365 restraints weight = 13608.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3772 rms_B_bonded: 2.17
r_work: 0.3537 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3518
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3518 r_free = 0.3518    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3518 r_free = 0.3518    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3518
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12267  Z= 0.166
  Angle     :  0.762   7.574  16656  Z= 0.371
  Chirality :  0.049   0.349   1908
  Planarity :  0.005   0.057   2013
  Dihedral  : 14.079  80.544   2145
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 13.78 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.40 (0.21), residues: 1392
  helix: -0.76 (0.17), residues: 924
  sheet: -4.26 (0.60), residues: 30
  loop : -3.05 (0.23), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 506 
 TYR   0.014   0.002   TYR C 177 
 PHE   0.016   0.002   PHE C  79 
 TRP   0.016   0.002   TRP C 180 
 HIS   0.007   0.001   HIS B 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (12267)
  covalent geometry    : angle       0.76201 (16656)
  hydrogen bonds       : bond        0.04951 (  597)
  hydrogen bonds       : angle       4.58288 ( 1755)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 143
  time to evaluate  : 0.426 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.8211 (mt) cc_final: 0.7924 (tp)
REVERT: A   69 GLU cc_start: 0.8065 (mp0) cc_final: 0.7519 (mp0)
REVERT: A  266 GLU cc_start: 0.7330 (tt0) cc_final: 0.7084 (tp30)
REVERT: A  292 TRP cc_start: 0.6906 (m100) cc_final: 0.6397 (m-10)
REVERT: B   69 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7563 (mp0)
REVERT: B  292 TRP cc_start: 0.6976 (m100) cc_final: 0.6475 (m-10)
REVERT: B  477 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7430 (tp)
REVERT: C   69 GLU cc_start: 0.8203 (mp0) cc_final: 0.7489 (mp0)
REVERT: C  292 TRP cc_start: 0.6847 (m100) cc_final: 0.6444 (m-10)
  outliers start: 43
  outliers final: 18
  residues processed: 177
  average time/residue: 0.4801
  time to fit residues: 93.8148
Evaluate side-chains
  143 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 PRO
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain B residue   36 PRO
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain B residue  359 LYS
Chi-restraints excluded: chain B residue  440 VAL
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  489 ILE
Chi-restraints excluded: chain C residue   36 PRO
Chi-restraints excluded: chain C residue  145 HIS
Chi-restraints excluded: chain C residue  178 CYS
Chi-restraints excluded: chain C residue  205 GLU
Chi-restraints excluded: chain C residue  340 LEU
Chi-restraints excluded: chain C residue  408 LEU
Chi-restraints excluded: chain C residue  440 VAL
Chi-restraints excluded: chain C residue  489 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   chunk 134 optimal weight:    0.0000
   chunk 49 optimal weight:    0.6980
   chunk 116 optimal weight:    6.9990
   chunk 118 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 194 HIS
** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.182811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.155354 restraints weight = 13667.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 2.17
r_work: 0.3475 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3495
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3495 r_free = 0.3495    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3495 r_free = 0.3495    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3495
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.3147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  12267  Z= 0.125
  Angle     :  0.672   7.683  16656  Z= 0.328
  Chirality :  0.046   0.332   1908
  Planarity :  0.004   0.052   2013
  Dihedral  : 12.377  70.994   2145
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 15.79 %
    Favored  : 81.01 %
  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 are not related in a simple way.
  whole: -1.64 (0.22), residues: 1392
  helix: -0.18 (0.17), residues: 924
  sheet: -4.11 (0.65), residues: 30
  loop : -2.74 (0.24), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 353 
 TYR   0.013   0.001   TYR B 249 
 PHE   0.010   0.001   PHE C  79 
 TRP   0.015   0.001   TRP C 180 
 HIS   0.004   0.001   HIS B 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (12267)
  covalent geometry    : angle       0.67158 (16656)
  hydrogen bonds       : bond        0.04106 (  597)
  hydrogen bonds       : angle       4.34704 ( 1755)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 135
  time to evaluate  : 0.426 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.8059 (mt) cc_final: 0.7787 (tp)
REVERT: A   69 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7579 (mp0)
REVERT: A  128 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6032 (pm20)
REVERT: A  193 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7267 (pp20)
REVERT: A  266 GLU cc_start: 0.7221 (tt0) cc_final: 0.7013 (tp30)
REVERT: A  292 TRP cc_start: 0.6887 (m100) cc_final: 0.6355 (m-10)
REVERT: B   69 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7595 (mp0)
REVERT: B  245 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7273 (mtp85)
REVERT: B  266 GLU cc_start: 0.7349 (tt0) cc_final: 0.7023 (tp30)
REVERT: B  292 TRP cc_start: 0.7004 (m100) cc_final: 0.6431 (m-10)
REVERT: B  477 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7386 (tp)
REVERT: C   69 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7334 (mp0)
REVERT: C  205 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6606 (pt0)
REVERT: C  292 TRP cc_start: 0.6907 (m100) cc_final: 0.6416 (m-10)
  outliers start: 40
  outliers final: 15
  residues processed: 167
  average time/residue: 0.4201
  time to fit residues: 78.2380
Evaluate side-chains
  146 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 GLU
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  149 LYS
Chi-restraints excluded: chain A residue  193 GLU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue  245 ARG
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  489 ILE
Chi-restraints excluded: chain C residue   69 GLU
Chi-restraints excluded: chain C residue  145 HIS
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  178 CYS
Chi-restraints excluded: chain C residue  203 LEU
Chi-restraints excluded: chain C residue  205 GLU
Chi-restraints excluded: chain C residue  340 LEU
Chi-restraints excluded: chain C residue  408 LEU
Chi-restraints excluded: chain C residue  489 ILE
Chi-restraints excluded: chain C residue  490 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 131 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 107 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 100 optimal weight:    0.4980
   chunk 53 optimal weight:    6.9990
   chunk 120 optimal weight:    4.9990
   chunk 115 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 355 ASN
** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.180664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.153026 restraints weight = 13637.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 2.12
r_work: 0.3443 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3487
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3487 r_free = 0.3487    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3487 r_free = 0.3487    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3487
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12267  Z= 0.152
  Angle     :  0.699   7.763  16656  Z= 0.340
  Chirality :  0.047   0.335   1908
  Planarity :  0.004   0.050   2013
  Dihedral  : 11.730  68.495   2145
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.89 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.51 %
    Favored  : 80.61 %
  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 are not related in a simple way.
  whole: -1.45 (0.22), residues: 1392
  helix: -0.06 (0.17), residues: 924
  sheet: -4.12 (0.65), residues: 30
  loop : -2.61 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 341 
 TYR   0.015   0.002   TYR B 249 
 PHE   0.011   0.001   PHE A 243 
 TRP   0.014   0.002   TRP A 180 
 HIS   0.006   0.001   HIS B 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (12267)
  covalent geometry    : angle       0.69902 (16656)
  hydrogen bonds       : bond        0.04314 (  597)
  hydrogen bonds       : angle       4.37715 ( 1755)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 130
  time to evaluate  : 0.413 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.8134 (mt) cc_final: 0.7875 (tp)
REVERT: A   69 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7512 (mp0)
REVERT: A  128 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6131 (pm20)
REVERT: A  266 GLU cc_start: 0.7187 (tt0) cc_final: 0.6982 (tp30)
REVERT: A  292 TRP cc_start: 0.7004 (m100) cc_final: 0.6417 (m-10)
REVERT: B   69 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7579 (mp0)
REVERT: B  245 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7400 (mtp85)
REVERT: B  266 GLU cc_start: 0.7409 (tt0) cc_final: 0.7042 (tp30)
REVERT: B  292 TRP cc_start: 0.7080 (m100) cc_final: 0.6467 (m-10)
REVERT: B  477 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7432 (tp)
REVERT: C   69 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7461 (mp0)
REVERT: C  292 TRP cc_start: 0.7053 (m100) cc_final: 0.6479 (m-10)
  outliers start: 36
  outliers final: 18
  residues processed: 159
  average time/residue: 0.4174
  time to fit residues: 74.0060
Evaluate side-chains
  143 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 119
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 PRO
Chi-restraints excluded: chain A residue   69 GLU
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue   36 PRO
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  245 ARG
Chi-restraints excluded: chain B residue  440 VAL
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  489 ILE
Chi-restraints excluded: chain C residue   36 PRO
Chi-restraints excluded: chain C residue   69 GLU
Chi-restraints excluded: chain C residue  145 HIS
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  340 LEU
Chi-restraints excluded: chain C residue  408 LEU
Chi-restraints excluded: chain C residue  440 VAL
Chi-restraints excluded: chain C residue  489 ILE
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  499 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 140 optimal weight:    0.4980
   chunk 17 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 107 optimal weight:    0.0060
   chunk 39 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0070
   chunk 83 optimal weight:    5.9990
   overall best weight:    0.9018

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

Flipped N/Q/H residues before XYZ refinement:
A 194 HIS
** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 429 HIS
** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.183032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.154166 restraints weight = 13640.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3752 rms_B_bonded: 2.30
r_work: 0.3514 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3529
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3529 r_free = 0.3529    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3529 r_free = 0.3529    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3529
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.3478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  12267  Z= 0.124
  Angle     :  0.645   7.956  16656  Z= 0.317
  Chirality :  0.044   0.266   1908
  Planarity :  0.004   0.051   2013
  Dihedral  : 11.061  67.347   2145
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 16.59 %
    Favored  : 80.37 %
  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 are not related in a simple way.
  whole: -1.10 (0.22), residues: 1392
  helix:  0.19 (0.17), residues: 924
  sheet: -4.10 (0.66), residues: 30
  loop : -2.41 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 462 
 TYR   0.015   0.001   TYR C 177 
 PHE   0.011   0.001   PHE C 368 
 TRP   0.013   0.001   TRP C 180 
 HIS   0.003   0.001   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (12267)
  covalent geometry    : angle       0.64505 (16656)
  hydrogen bonds       : bond        0.03951 (  597)
  hydrogen bonds       : angle       4.23572 ( 1755)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 137
  time to evaluate  : 0.460 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.8049 (mt) cc_final: 0.7815 (tp)
REVERT: A   69 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7443 (mp0)
REVERT: A  128 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6178 (pm20)
REVERT: A  292 TRP cc_start: 0.7052 (m100) cc_final: 0.6428 (m-10)
REVERT: B   69 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7435 (mp0)
REVERT: B  128 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.5417 (pm20)
REVERT: B  266 GLU cc_start: 0.7399 (tt0) cc_final: 0.7047 (tp30)
REVERT: B  292 TRP cc_start: 0.7066 (m100) cc_final: 0.6428 (m-10)
REVERT: B  477 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7425 (tp)
REVERT: C   69 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7386 (mp0)
REVERT: C  128 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6890 (mp0)
REVERT: C  159 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8247 (tm-30)
REVERT: C  292 TRP cc_start: 0.7000 (m100) cc_final: 0.6384 (m-10)
  outliers start: 38
  outliers final: 21
  residues processed: 166
  average time/residue: 0.4915
  time to fit residues: 90.3785
Evaluate side-chains
  155 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 127
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 GLU
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain B residue  289 ARG
Chi-restraints excluded: chain B residue  440 VAL
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  489 ILE
Chi-restraints excluded: chain C residue   69 GLU
Chi-restraints excluded: chain C residue  128 GLU
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  245 ARG
Chi-restraints excluded: chain C residue  340 LEU
Chi-restraints excluded: chain C residue  388 LEU
Chi-restraints excluded: chain C residue  408 LEU
Chi-restraints excluded: chain C residue  440 VAL
Chi-restraints excluded: chain C residue  489 ILE
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  499 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 130 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 132 optimal weight:    1.9990
   chunk 79 optimal weight:    7.9990
   chunk 45 optimal weight:    4.9990
   chunk 127 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9990
   chunk 134 optimal weight:    0.0870
   overall best weight:    1.6166

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
C 355 ASN
C 455 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.179247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.150554 restraints weight = 13692.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 2.29
r_work: 0.3459 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3432
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3432 r_free = 0.3432    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3432 r_free = 0.3432    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3432
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.3548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  12267  Z= 0.159
  Angle     :  0.699   6.500  16656  Z= 0.342
  Chirality :  0.046   0.249   1908
  Planarity :  0.004   0.048   2013
  Dihedral  : 11.018  70.499   2145
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 17.07 %
    Favored  : 79.89 %
  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 are not related in a simple way.
  whole: -1.14 (0.22), residues: 1392
  helix:  0.14 (0.17), residues: 927
  sheet: -4.10 (0.63), residues: 30
  loop : -2.39 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 322 
 TYR   0.017   0.002   TYR B 249 
 PHE   0.019   0.002   PHE C 298 
 TRP   0.013   0.002   TRP A 180 
 HIS   0.006   0.001   HIS B 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (12267)
  covalent geometry    : angle       0.69923 (16656)
  hydrogen bonds       : bond        0.04322 (  597)
  hydrogen bonds       : angle       4.34495 ( 1755)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 146
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.8188 (mt) cc_final: 0.7945 (tp)
REVERT: A   63 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7704 (tp)
REVERT: A   69 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7550 (mp0)
REVERT: A  128 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6167 (pm20)
REVERT: A  159 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8332 (tm-30)
REVERT: A  188 VAL cc_start: 0.7529 (p) cc_final: 0.7071 (t)
REVERT: A  292 TRP cc_start: 0.7132 (m100) cc_final: 0.6455 (m-10)
REVERT: B   69 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7592 (mp0)
REVERT: B  128 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6680 (mp0)
REVERT: B  266 GLU cc_start: 0.7514 (tt0) cc_final: 0.7132 (tp30)
REVERT: B  292 TRP cc_start: 0.7155 (m100) cc_final: 0.6458 (m-10)
REVERT: B  477 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7459 (tp)
REVERT: C   69 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7669 (mp0)
REVERT: C  128 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6937 (mp0)
REVERT: C  159 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8267 (tm-30)
REVERT: C  203 LEU cc_start: 0.2515 (OUTLIER) cc_final: 0.2314 (mt)
REVERT: C  266 GLU cc_start: 0.7342 (tt0) cc_final: 0.7028 (mm-30)
REVERT: C  292 TRP cc_start: 0.7114 (m100) cc_final: 0.6395 (m-10)
  outliers start: 38
  outliers final: 20
  residues processed: 175
  average time/residue: 0.4806
  time to fit residues: 92.9847
Evaluate side-chains
  167 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 138
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 PRO
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   69 GLU
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  489 ILE
Chi-restraints excluded: chain C residue   69 GLU
Chi-restraints excluded: chain C residue  128 GLU
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  203 LEU
Chi-restraints excluded: chain C residue  245 ARG
Chi-restraints excluded: chain C residue  340 LEU
Chi-restraints excluded: chain C residue  388 LEU
Chi-restraints excluded: chain C residue  408 LEU
Chi-restraints excluded: chain C residue  440 VAL
Chi-restraints excluded: chain C residue  489 ILE
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  499 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 124 optimal weight:    0.6980
   chunk 80 optimal weight:    4.9990
   chunk 90 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 130 optimal weight:    5.9990
   chunk 41 optimal weight:    4.9990
   chunk 140 optimal weight:    9.9990
   chunk 129 optimal weight:    0.7980
   chunk 69 optimal weight:    5.9990
   chunk 74 optimal weight:    7.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    1.2382

-------------------------------------------------------------------------------
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 = 0.3972 r_free = 0.3972 target = 0.180735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.152976 restraints weight = 13549.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 2.13
r_work: 0.3438 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3472
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3472 r_free = 0.3472    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3472 r_free = 0.3472    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3472
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  12267  Z= 0.137
  Angle     :  0.664   6.393  16656  Z= 0.327
  Chirality :  0.044   0.229   1908
  Planarity :  0.004   0.049   2013
  Dihedral  : 10.919  69.327   2145
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 18.11 %
    Favored  : 79.25 %
  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 are not related in a simple way.
  whole: -0.99 (0.22), residues: 1392
  helix:  0.28 (0.17), residues: 927
  sheet: -4.09 (0.64), residues: 30
  loop : -2.39 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 462 
 TYR   0.019   0.001   TYR B 249 
 PHE   0.028   0.001   PHE C 298 
 TRP   0.013   0.001   TRP C 180 
 HIS   0.005   0.001   HIS B 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (12267)
  covalent geometry    : angle       0.66350 (16656)
  hydrogen bonds       : bond        0.04079 (  597)
  hydrogen bonds       : angle       4.28053 ( 1755)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 143
  time to evaluate  : 0.470 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.8119 (mt) cc_final: 0.7866 (tp)
REVERT: A   69 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7477 (mp0)
REVERT: A  128 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6231 (pm20)
REVERT: A  188 VAL cc_start: 0.7526 (p) cc_final: 0.7037 (t)
REVERT: A  292 TRP cc_start: 0.7070 (m100) cc_final: 0.6360 (m-10)
REVERT: B   69 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7503 (mp0)
REVERT: B  128 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6694 (mp0)
REVERT: B  182 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6437 (mt-10)
REVERT: B  188 VAL cc_start: 0.7231 (p) cc_final: 0.6733 (t)
REVERT: B  266 GLU cc_start: 0.7470 (tt0) cc_final: 0.7143 (tp30)
REVERT: B  289 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.6526 (ptm160)
REVERT: B  292 TRP cc_start: 0.7163 (m100) cc_final: 0.6450 (m-10)
REVERT: B  439 ARG cc_start: 0.7419 (ptp-170) cc_final: 0.7038 (ptm160)
REVERT: B  477 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7463 (tp)
REVERT: C   69 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7657 (mp0)
REVERT: C  128 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6988 (mp0)
REVERT: C  159 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8256 (tm-30)
REVERT: C  203 LEU cc_start: 0.2294 (OUTLIER) cc_final: 0.2039 (mt)
REVERT: C  266 GLU cc_start: 0.7308 (tt0) cc_final: 0.7056 (mm-30)
REVERT: C  292 TRP cc_start: 0.7144 (m100) cc_final: 0.6399 (m-10)
  outliers start: 33
  outliers final: 16
  residues processed: 168
  average time/residue: 0.4685
  time to fit residues: 87.3642
Evaluate side-chains
  158 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 GLU
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain B residue  289 ARG
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  489 ILE
Chi-restraints excluded: chain C residue   69 GLU
Chi-restraints excluded: chain C residue  128 GLU
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  203 LEU
Chi-restraints excluded: chain C residue  245 ARG
Chi-restraints excluded: chain C residue  340 LEU
Chi-restraints excluded: chain C residue  388 LEU
Chi-restraints excluded: chain C residue  408 LEU
Chi-restraints excluded: chain C residue  440 VAL
Chi-restraints excluded: chain C residue  489 ILE
Chi-restraints excluded: chain C residue  490 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 52 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 117 optimal weight:    4.9990
   chunk 56 optimal weight:    5.9990
   chunk 120 optimal weight:    0.0010
   chunk 4 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.7588

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

Flipped N/Q/H residues before XYZ refinement:
B  55 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.183075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.155585 restraints weight = 13531.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 2.18
r_work: 0.3530 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3562
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3562
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.3789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12267  Z= 0.118
  Angle     :  0.632   8.665  16656  Z= 0.313
  Chirality :  0.043   0.197   1908
  Planarity :  0.004   0.051   2013
  Dihedral  : 10.787  69.550   2145
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 19.15 %
    Favored  : 78.61 %
  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 are not related in a simple way.
  whole: -0.72 (0.22), residues: 1392
  helix:  0.49 (0.17), residues: 927
  sheet: -4.00 (0.65), residues: 30
  loop : -2.30 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 462 
 TYR   0.018   0.001   TYR B 249 
 PHE   0.030   0.001   PHE C 298 
 TRP   0.013   0.001   TRP C 180 
 HIS   0.005   0.001   HIS C 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (12267)
  covalent geometry    : angle       0.63243 (16656)
  hydrogen bonds       : bond        0.03866 (  597)
  hydrogen bonds       : angle       4.18959 ( 1755)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 136
  time to evaluate  : 0.440 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.8046 (mt) cc_final: 0.7797 (tp)
REVERT: A   69 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7360 (mp0)
REVERT: A  128 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6235 (pm20)
REVERT: A  159 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8245 (tm-30)
REVERT: A  292 TRP cc_start: 0.6990 (m100) cc_final: 0.6246 (m-10)
REVERT: A  422 ARG cc_start: 0.7910 (mmt180) cc_final: 0.7704 (mmt-90)
REVERT: B   69 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7408 (mp0)
REVERT: B  128 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.5429 (pm20)
REVERT: B  159 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8089 (tm-30)
REVERT: B  182 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6492 (mt-10)
REVERT: B  188 VAL cc_start: 0.7196 (p) cc_final: 0.6736 (t)
REVERT: B  266 GLU cc_start: 0.7393 (tt0) cc_final: 0.7101 (tp30)
REVERT: B  292 TRP cc_start: 0.7118 (m100) cc_final: 0.6405 (m-10)
REVERT: B  422 ARG cc_start: 0.7986 (mmt-90) cc_final: 0.7742 (mmt-90)
REVERT: B  477 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7438 (tp)
REVERT: C   69 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7431 (mp0)
REVERT: C  128 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7056 (mp0)
REVERT: C  159 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8184 (tm-30)
REVERT: C  266 GLU cc_start: 0.7222 (tt0) cc_final: 0.6995 (mm-30)
REVERT: C  292 TRP cc_start: 0.7020 (m100) cc_final: 0.6349 (m-10)
  outliers start: 28
  outliers final: 13
  residues processed: 155
  average time/residue: 0.4834
  time to fit residues: 82.6550
Evaluate side-chains
  156 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 GLU
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  489 ILE
Chi-restraints excluded: chain C residue   69 GLU
Chi-restraints excluded: chain C residue  128 GLU
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  245 ARG
Chi-restraints excluded: chain C residue  340 LEU
Chi-restraints excluded: chain C residue  408 LEU
Chi-restraints excluded: chain C residue  440 VAL
Chi-restraints excluded: chain C residue  489 ILE
Chi-restraints excluded: chain C residue  490 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 139 optimal weight:    4.9990
   chunk 124 optimal weight:    3.9990
   chunk 140 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 115 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 137 optimal weight:    3.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 455 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.179072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.151470 restraints weight = 13613.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3727 rms_B_bonded: 2.24
r_work: 0.3482 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3486
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3486
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.3746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  12267  Z= 0.175
  Angle     :  0.701   7.890  16656  Z= 0.344
  Chirality :  0.046   0.274   1908
  Planarity :  0.004   0.049   2013
  Dihedral  : 10.920  71.275   2145
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 19.15 %
    Favored  : 78.53 %
  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 are not related in a simple way.
  whole: -0.95 (0.22), residues: 1392
  helix:  0.30 (0.17), residues: 927
  sheet: -4.04 (0.63), residues: 30
  loop : -2.35 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 341 
 TYR   0.021   0.002   TYR B 249 
 PHE   0.030   0.002   PHE C 298 
 TRP   0.013   0.002   TRP A 180 
 HIS   0.007   0.001   HIS B 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 (12267)
  covalent geometry    : angle       0.70090 (16656)
  hydrogen bonds       : bond        0.04333 (  597)
  hydrogen bonds       : angle       4.34585 ( 1755)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 139
  time to evaluate  : 0.394 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.8154 (mt) cc_final: 0.7901 (tp)
REVERT: A   69 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7463 (mp0)
REVERT: A  128 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6223 (pm20)
REVERT: A  159 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8289 (tm-30)
REVERT: A  193 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7513 (pp20)
REVERT: A  292 TRP cc_start: 0.7072 (m100) cc_final: 0.6341 (m-10)
REVERT: B   69 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7487 (mp0)
REVERT: B  159 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8150 (tm-30)
REVERT: B  182 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6540 (mt-10)
REVERT: B  266 GLU cc_start: 0.7385 (tt0) cc_final: 0.7087 (tp30)
REVERT: B  439 ARG cc_start: 0.7351 (ptp-170) cc_final: 0.6958 (ptm160)
REVERT: B  477 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7475 (tp)
REVERT: C   69 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7684 (mp0)
REVERT: C  128 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6957 (mp0)
REVERT: C  159 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8230 (tm-30)
REVERT: C  266 GLU cc_start: 0.7277 (tt0) cc_final: 0.7044 (mm-30)
REVERT: C  292 TRP cc_start: 0.7120 (m100) cc_final: 0.6379 (m-10)
  outliers start: 29
  outliers final: 14
  residues processed: 160
  average time/residue: 0.4716
  time to fit residues: 83.5365
Evaluate side-chains
  159 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 137
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 GLU
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  193 GLU
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  489 ILE
Chi-restraints excluded: chain C residue   69 GLU
Chi-restraints excluded: chain C residue  128 GLU
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  245 ARG
Chi-restraints excluded: chain C residue  340 LEU
Chi-restraints excluded: chain C residue  388 LEU
Chi-restraints excluded: chain C residue  408 LEU
Chi-restraints excluded: chain C residue  440 VAL
Chi-restraints excluded: chain C residue  490 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0980
   chunk 25 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   chunk 131 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 93 optimal weight:    0.3980
   chunk 4 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 134 optimal weight:    0.0670
   chunk 101 optimal weight:    3.9990
   overall best weight:    0.9122

-------------------------------------------------------------------------------
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 = 0.3994 r_free = 0.3994 target = 0.182731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.155304 restraints weight = 13604.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 2.13
r_work: 0.3468 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3517
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3517 r_free = 0.3517    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3517 r_free = 0.3517    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3517
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.3867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12267  Z= 0.124
  Angle     :  0.644   9.259  16656  Z= 0.319
  Chirality :  0.043   0.201   1908
  Planarity :  0.004   0.044   2013
  Dihedral  : 10.817  69.292   2145
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 19.79 %
    Favored  : 78.21 %
  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 are not related in a simple way.
  whole: -0.72 (0.22), residues: 1392
  helix:  0.48 (0.17), residues: 927
  sheet: -4.01 (0.64), residues: 30
  loop : -2.27 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 462 
 TYR   0.019   0.001   TYR B 249 
 PHE   0.029   0.001   PHE C 298 
 TRP   0.013   0.001   TRP C 180 
 HIS   0.004   0.001   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (12267)
  covalent geometry    : angle       0.64365 (16656)
  hydrogen bonds       : bond        0.03918 (  597)
  hydrogen bonds       : angle       4.22531 ( 1755)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3777.58 seconds
wall clock time: 65 minutes 11.62 seconds (3911.62 seconds total)