Starting phenix.real_space_refine
on Fri Sep 11 21:57:55 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6wr4_21876/09_2026/6wr4_21876.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wr4_21876/09_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wr4_21876/09_2026/6wr4_21876.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wr4_21876/09_2026/6wr4_21876.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/6wr4_21876/09_2026/6wr4_21876.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6wr4_21876/09_2026/6wr4_21876.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wr4_21876/09_2026/6wr4_21876.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wr4_21876/09_2026/6wr4_21876.cif"
  }
  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): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 1
          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: 3.90, per 1000 atoms: 0.33
  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: 1.02
  Conformation dependent library (CDL) restraints added in 582.1 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: 0.32
  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: 1.37 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 -    20.70: 6564
       20.70 -    41.40: 378
       41.40 -    62.09: 78
       62.09 -    82.79: 21
       82.79 -   103.49: 6
  Dihedral angle restraints: 7047
    sinusoidal: 2901
      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 7044 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:             0.710
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.250
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
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  : 14.492 103.490   4359
  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/Z
  covalent geometry    : bond        0.01174 /  0.56 (12267)
  covalent geometry    : angle       1.39823 /  0.74 (16656)
  hydrogen bonds       : bond        0.30275 / 19.20 (  597)
  hydrogen bonds       : angle      10.16717 /  7.09 ( 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  : 0.434 
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: 0.5144
  time to fit residues: 175.6929
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  : 0.428 
-------------------------------------------------------------------------------
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...
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 = 0.185801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.158089 restraints weight = 13479.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 2.17
r_work: 0.3505 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3480
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3480 r_free = 0.3480    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3479 r_free = 0.3479    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (11 function evaluations)
r_final: 0.3479
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.2283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12267  Z= 0.152
  Angle     :  0.764   8.368  16656  Z= 0.387
  Chirality :  0.045   0.169   1908
  Planarity :  0.006   0.059   2013
  Dihedral  : 11.263  69.881   1667
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 10.26 %
    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: -3.55 (0.19), residues: 1392
  helix: -1.82 (0.15), residues: 939
  sheet: -4.51 (0.56), residues: 30
  loop : -3.08 (0.24), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 214 
 TYR   0.016   0.001   TYR A 177 
 PHE   0.013   0.001   PHE A  79 
 TRP   0.014   0.001   TRP C 180 
 HIS   0.005   0.001   HIS B 406 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.15 (12267)
  covalent geometry    : angle       0.76390 /  0.39 (16656)
  hydrogen bonds       : bond        0.05498 /  3.46 (  597)
  hydrogen bonds       : angle       4.93274 /  3.47 ( 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
  212 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 175
  time to evaluate  : 0.466 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.7963 (mt) cc_final: 0.7658 (tp)
REVERT: A  292 TRP cc_start: 0.6941 (m100) cc_final: 0.6448 (m-10)
REVERT: B  292 TRP cc_start: 0.7148 (m100) cc_final: 0.6683 (m-10)
REVERT: B  422 ARG cc_start: 0.7812 (mmt-90) cc_final: 0.7586 (mmt180)
REVERT: C  292 TRP cc_start: 0.6996 (m100) cc_final: 0.6518 (m-10)
  outliers start: 37
  outliers final: 11
  residues processed: 199
  average time/residue: 0.4755
  time to fit residues: 104.2212
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  : 0.365 
-------------------------------------------------------------------------------
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 B residue  205 GLU
Chi-restraints excluded: chain C residue   36 PRO
Chi-restraints excluded: chain C residue  145 HIS
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:    0.2980
   chunk 65 optimal weight:    0.3980
   chunk 140 optimal weight:    2.9990
   chunk 86 optimal weight:    6.9990
   chunk 96 optimal weight:    8.9990
   chunk 19 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 121 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 32 optimal weight:    9.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  57 ASN
** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 250 ASN
** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 455 ASN
B  57 ASN
** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 250 ASN
** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 250 ASN
** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.182494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.154074 restraints weight = 13595.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3807 rms_B_bonded: 2.31
r_work: 0.3585 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3540
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    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 = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (23 function evaluations)
r_final: 0.3540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.2745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  12267  Z= 0.139
  Angle     :  0.698   7.539  16656  Z= 0.348
  Chirality :  0.045   0.206   1908
  Planarity :  0.005   0.052   2013
  Dihedral  :  9.984  67.274   1659
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 14.18 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -2.30 (0.21), residues: 1392
  helix: -0.69 (0.17), residues: 924
  sheet: -4.21 (0.63), residues: 30
  loop : -3.01 (0.23), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 214 
 TYR   0.014   0.001   TYR A 177 
 PHE   0.013   0.001   PHE C  79 
 TRP   0.015   0.002   TRP C 180 
 HIS   0.005   0.001   HIS B 348 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.14 (12267)
  covalent geometry    : angle       0.69781 /  0.35 (16656)
  hydrogen bonds       : bond        0.04609 /  2.91 (  597)
  hydrogen bonds       : angle       4.48602 /  3.16 ( 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
  183 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 144
  time to evaluate  : 0.469 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.8089 (mt) cc_final: 0.7810 (tp)
REVERT: A   69 GLU cc_start: 0.8017 (mp0) cc_final: 0.7472 (mp0)
REVERT: A  266 GLU cc_start: 0.7288 (tt0) cc_final: 0.7075 (tp30)
REVERT: A  292 TRP cc_start: 0.6850 (m100) cc_final: 0.6370 (m-10)
REVERT: B   69 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7578 (mp0)
REVERT: B  292 TRP cc_start: 0.6911 (m100) cc_final: 0.6443 (m-10)
REVERT: B  477 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7473 (tp)
REVERT: C   69 GLU cc_start: 0.8090 (mp0) cc_final: 0.7324 (mp0)
REVERT: C  292 TRP cc_start: 0.6827 (m100) cc_final: 0.6374 (m-10)
  outliers start: 39
  outliers final: 17
  residues processed: 170
  average time/residue: 0.4291
  time to fit residues: 81.5177
Evaluate side-chains
  143 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 PRO
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  245 ARG
Chi-restraints excluded: chain B residue  408 LEU
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:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 75 optimal weight:    0.6980
   chunk 134 optimal weight:    0.0040
   chunk 49 optimal weight:    5.9990
   chunk 116 optimal weight:    0.5980
   chunk 118 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.8394

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 355 ASN
** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 351 GLN
B 406 HIS
** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.186625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.159773 restraints weight = 13523.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 2.08
r_work: 0.3499 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3588
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3588 r_free = 0.3588    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3588 r_free = 0.3588    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3588
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.3109

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= 0.119
  Angle     :  0.636   6.759  16656  Z= 0.317
  Chirality :  0.043   0.204   1908
  Planarity :  0.004   0.049   2013
  Dihedral  :  9.243  59.743   1659
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 15.38 %
    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: -1.51 (0.22), residues: 1392
  helix: -0.08 (0.17), residues: 924
  sheet: -4.06 (0.67), residues: 30
  loop : -2.70 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 462 
 TYR   0.013   0.001   TYR C 177 
 PHE   0.009   0.001   PHE C  79 
 TRP   0.014   0.001   TRP C 180 
 HIS   0.005   0.001   HIS B 406 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.12 (12267)
  covalent geometry    : angle       0.63559 /  0.32 (16656)
  hydrogen bonds       : bond        0.04047 /  2.57 (  597)
  hydrogen bonds       : angle       4.29369 /  3.02 ( 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
  191 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 146
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.8040 (mt) cc_final: 0.7773 (tp)
REVERT: A   69 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7451 (mp0)
REVERT: A  128 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6032 (pm20)
REVERT: A  292 TRP cc_start: 0.6870 (m100) cc_final: 0.6374 (m-10)
REVERT: B   69 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7501 (mp0)
REVERT: B  266 GLU cc_start: 0.7254 (tt0) cc_final: 0.6908 (tp30)
REVERT: B  292 TRP cc_start: 0.6929 (m100) cc_final: 0.6386 (m-10)
REVERT: B  433 CYS cc_start: 0.7083 (m) cc_final: 0.6773 (m)
REVERT: B  477 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7353 (tp)
REVERT: C   69 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7273 (mp0)
REVERT: C  292 TRP cc_start: 0.6859 (m100) cc_final: 0.6387 (m-10)
  outliers start: 45
  outliers final: 16
  residues processed: 181
  average time/residue: 0.3808
  time to fit residues: 77.4437
Evaluate side-chains
  151 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 130
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
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  489 ILE
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  359 LYS
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  178 CYS
Chi-restraints excluded: chain C residue  203 LEU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 131 optimal weight:    5.9990
   chunk 96 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 100 optimal weight:    0.1980
   chunk 53 optimal weight:    0.2980
   chunk 120 optimal weight:    2.9990
   chunk 115 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0870
   overall best weight:    0.4758

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 194 HIS
B 194 HIS
** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 284 GLN
** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.188863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.160913 restraints weight = 13491.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 2.15
r_work: 0.3525 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3553
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3553 r_free = 0.3553    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3553 r_free = 0.3553    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3553
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.3378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  12267  Z= 0.112
  Angle     :  0.609   7.106  16656  Z= 0.305
  Chirality :  0.042   0.172   1908
  Planarity :  0.004   0.046   2013
  Dihedral  :  8.391  60.714   1659
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  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: -0.94 (0.22), residues: 1392
  helix:  0.36 (0.18), residues: 912
  sheet: -4.00 (0.68), residues: 30
  loop : -2.41 (0.25), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 462 
 TYR   0.012   0.001   TYR C 177 
 PHE   0.009   0.001   PHE A 242 
 TRP   0.012   0.001   TRP C  37 
 HIS   0.003   0.001   HIS A  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00236 /  0.11 (12267)
  covalent geometry    : angle       0.60879 /  0.30 (16656)
  hydrogen bonds       : bond        0.03764 /  2.39 (  597)
  hydrogen bonds       : angle       4.17556 /  2.94 ( 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
  176 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 138
  time to evaluate  : 0.445 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.7992 (mt) cc_final: 0.7734 (tp)
REVERT: A   69 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7406 (mp0)
REVERT: A  292 TRP cc_start: 0.6848 (m100) cc_final: 0.6295 (m-10)
REVERT: B   69 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7418 (mp0)
REVERT: B  128 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.5400 (pm20)
REVERT: B  245 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7222 (mtp85)
REVERT: B  266 GLU cc_start: 0.7259 (tt0) cc_final: 0.6932 (tp30)
REVERT: B  292 TRP cc_start: 0.6899 (m100) cc_final: 0.6372 (m-10)
REVERT: B  477 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7382 (tp)
REVERT: C   69 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7191 (mp0)
REVERT: C  128 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6875 (mp0)
REVERT: C  159 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8261 (tm-30)
REVERT: C  292 TRP cc_start: 0.6867 (m100) cc_final: 0.6354 (m-10)
  outliers start: 38
  outliers final: 12
  residues processed: 165
  average time/residue: 0.4459
  time to fit residues: 81.7395
Evaluate side-chains
  139 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 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 B residue   69 GLU
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  245 ARG
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   69 GLU
Chi-restraints excluded: chain C residue  128 GLU
Chi-restraints excluded: chain C residue  145 HIS
Chi-restraints excluded: chain C residue  205 GLU
Chi-restraints excluded: chain C residue  408 LEU
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:    0.9980
   chunk 42 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 140 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 107 optimal weight:    0.8980
   chunk 39 optimal weight:   10.0000
   chunk 59 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    1.5184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 355 ASN
B 429 HIS
C 355 ASN
C 455 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.181165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.153339 restraints weight = 13536.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 2.14
r_work: 0.3471 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3496
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3496 r_free = 0.3496    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3496 r_free = 0.3496    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3496
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.3405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12267  Z= 0.154
  Angle     :  0.677   6.695  16656  Z= 0.334
  Chirality :  0.045   0.251   1908
  Planarity :  0.004   0.048   2013
  Dihedral  :  8.401  69.486   1659
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 17.07 %
    Favored  : 80.21 %
  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: -1.06 (0.22), residues: 1392
  helix:  0.17 (0.17), residues: 945
  sheet: -4.09 (0.65), residues: 30
  loop : -2.37 (0.27), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 341 
 TYR   0.015   0.002   TYR C 177 
 PHE   0.022   0.002   PHE C  73 
 TRP   0.013   0.002   TRP A 180 
 HIS   0.005   0.001   HIS B 348 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.15 (12267)
  covalent geometry    : angle       0.67736 /  0.33 (16656)
  hydrogen bonds       : bond        0.04258 /  2.67 (  597)
  hydrogen bonds       : angle       4.29661 /  3.02 ( 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
  176 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 142
  time to evaluate  : 0.434 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.8161 (mt) cc_final: 0.7917 (tp)
REVERT: A   69 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7520 (mp0)
REVERT: A  128 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6174 (pm20)
REVERT: A  159 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8292 (tm-30)
REVERT: A  292 TRP cc_start: 0.7074 (m100) cc_final: 0.6486 (m-10)
REVERT: B   69 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7613 (mp0)
REVERT: B  128 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.5444 (pm20)
REVERT: B  245 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7323 (mtp85)
REVERT: B  266 GLU cc_start: 0.7337 (tt0) cc_final: 0.6985 (tp30)
REVERT: B  292 TRP cc_start: 0.7097 (m100) cc_final: 0.6463 (m-10)
REVERT: B  477 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7467 (tp)
REVERT: C   69 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7448 (mp0)
REVERT: C  128 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6925 (mp0)
REVERT: C  159 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8264 (tm-30)
REVERT: C  292 TRP cc_start: 0.7049 (m100) cc_final: 0.6450 (m-10)
  outliers start: 34
  outliers final: 16
  residues processed: 168
  average time/residue: 0.4472
  time to fit residues: 83.3927
Evaluate side-chains
  146 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
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 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  203 LEU
Chi-restraints excluded: chain B residue  245 ARG
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   69 GLU
Chi-restraints excluded: chain C residue  128 GLU
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  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:    0.8980
   chunk 130 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   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:    0.9990
   chunk 127 optimal weight:    0.7980
   chunk 90 optimal weight:    1.9990
   chunk 134 optimal weight:    2.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 428 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.181684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.153602 restraints weight = 13593.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 2.14
r_work: 0.3493 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3498
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3498
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12267  Z= 0.131
  Angle     :  0.640   6.396  16656  Z= 0.317
  Chirality :  0.043   0.201   1908
  Planarity :  0.004   0.049   2013
  Dihedral  :  8.133  69.833   1659
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 17.47 %
    Favored  : 79.49 %
  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: -0.91 (0.22), residues: 1392
  helix:  0.34 (0.17), residues: 927
  sheet: -4.06 (0.66), residues: 30
  loop : -2.33 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 462 
 TYR   0.016   0.001   TYR C 177 
 PHE   0.027   0.001   PHE C 298 
 TRP   0.011   0.001   TRP A 180 
 HIS   0.005   0.001   HIS B 348 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.13 (12267)
  covalent geometry    : angle       0.64009 /  0.32 (16656)
  hydrogen bonds       : bond        0.03979 /  2.51 (  597)
  hydrogen bonds       : angle       4.22902 /  2.98 ( 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
  174 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 136
  time to evaluate  : 0.428 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.8091 (mt) cc_final: 0.7844 (tp)
REVERT: A   69 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7477 (mp0)
REVERT: A  128 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6226 (pm20)
REVERT: A  159 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8242 (tm-30)
REVERT: A  292 TRP cc_start: 0.7006 (m100) cc_final: 0.6402 (m-10)
REVERT: B   69 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7557 (mp0)
REVERT: B  128 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.5529 (pm20)
REVERT: B  245 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7201 (mtp85)
REVERT: B  266 GLU cc_start: 0.7320 (tt0) cc_final: 0.6999 (tp30)
REVERT: B  292 TRP cc_start: 0.7133 (m100) cc_final: 0.6508 (m-10)
REVERT: B  477 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7451 (tp)
REVERT: B  508 PHE cc_start: 0.7351 (m-80) cc_final: 0.7130 (m-80)
REVERT: C   69 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7474 (mp0)
REVERT: C  128 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6937 (mp0)
REVERT: C  159 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8225 (tm-30)
REVERT: C  266 GLU cc_start: 0.7274 (tt0) cc_final: 0.6976 (mm-30)
REVERT: C  292 TRP cc_start: 0.7050 (m100) cc_final: 0.6420 (m-10)
  outliers start: 38
  outliers final: 18
  residues processed: 164
  average time/residue: 0.4445
  time to fit residues: 81.2690
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  : 0.438 
-------------------------------------------------------------------------------
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  245 ARG
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 B residue  499 LEU
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  340 LEU
Chi-restraints excluded: chain C residue  388 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 124 optimal weight:    0.5980
   chunk 80 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 130 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 140 optimal weight:    0.2980
   chunk 129 optimal weight:    1.9990
   chunk 69 optimal weight:    7.9990
   chunk 74 optimal weight:    0.0870
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.4558

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  55 GLN
C 351 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.185465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.157852 restraints weight = 13480.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3772 rms_B_bonded: 2.13
r_work: 0.3537 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3622
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3622 r_free = 0.3622    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3622 r_free = 0.3622    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3622
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.3739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  12267  Z= 0.108
  Angle     :  0.597   6.116  16656  Z= 0.297
  Chirality :  0.041   0.202   1908
  Planarity :  0.004   0.045   2013
  Dihedral  :  7.760  70.660   1659
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 18.75 %
    Favored  : 79.33 %
  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: -0.55 (0.23), residues: 1392
  helix:  0.57 (0.17), residues: 945
  sheet: -4.02 (0.68), residues: 30
  loop : -2.19 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 462 
 TYR   0.013   0.001   TYR C 177 
 PHE   0.029   0.001   PHE C 298 
 TRP   0.011   0.001   TRP C 180 
 HIS   0.003   0.001   HIS C 444 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00229 /  0.11 (12267)
  covalent geometry    : angle       0.59704 /  0.30 (16656)
  hydrogen bonds       : bond        0.03611 /  2.29 (  597)
  hydrogen bonds       : angle       4.08941 /  2.88 ( 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
  167 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 143
  time to evaluate  : 0.436 
Fit side-chains
REVERT: A   69 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7278 (mp0)
REVERT: A  128 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6260 (pm20)
REVERT: A  159 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8086 (tm-30)
REVERT: A  188 VAL cc_start: 0.7460 (p) cc_final: 0.6979 (t)
REVERT: A  292 TRP cc_start: 0.6904 (m100) cc_final: 0.6339 (m-10)
REVERT: B   69 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7460 (mp0)
REVERT: B  159 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8094 (tm-30)
REVERT: B  188 VAL cc_start: 0.7534 (p) cc_final: 0.7057 (t)
REVERT: B  266 GLU cc_start: 0.7251 (tt0) cc_final: 0.7004 (tp30)
REVERT: B  292 TRP cc_start: 0.7043 (m100) cc_final: 0.6444 (m-10)
REVERT: B  422 ARG cc_start: 0.7718 (mmt-90) cc_final: 0.7452 (mmt180)
REVERT: B  477 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7440 (tp)
REVERT: C   69 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7300 (mp0)
REVERT: C  159 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8201 (tm-30)
REVERT: C  280 LEU cc_start: 0.7375 (tp) cc_final: 0.6763 (mp)
REVERT: C  292 TRP cc_start: 0.6979 (m100) cc_final: 0.6378 (m-10)
  outliers start: 24
  outliers final: 12
  residues processed: 159
  average time/residue: 0.3763
  time to fit residues: 67.6151
Evaluate side-chains
  148 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
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  203 LEU
Chi-restraints excluded: chain B residue  245 ARG
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   69 GLU
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  408 LEU
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:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9980
   chunk 93 optimal weight:    0.0030
   chunk 117 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 120 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 9 optimal weight:    8.9990
   chunk 90 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   overall best weight:    1.7996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3961 r_free = 0.3961 target = 0.179640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.150697 restraints weight = 13513.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 2.27
r_work: 0.3416 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3467
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3467 r_free = 0.3467    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3467 r_free = 0.3467    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3467
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.3653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12267  Z= 0.169
  Angle     :  0.691   7.228  16656  Z= 0.339
  Chirality :  0.046   0.274   1908
  Planarity :  0.004   0.046   2013
  Dihedral  :  8.181  73.939   1659
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 18.75 %
    Favored  : 78.85 %
  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: -0.80 (0.22), residues: 1392
  helix:  0.36 (0.17), residues: 945
  sheet: -4.01 (0.65), residues: 30
  loop : -2.23 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 462 
 TYR   0.018   0.002   TYR C 177 
 PHE   0.029   0.002   PHE C 298 
 TRP   0.012   0.002   TRP A 180 
 HIS   0.006   0.001   HIS B 348 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00407 /  0.17 (12267)
  covalent geometry    : angle       0.69122 /  0.34 (16656)
  hydrogen bonds       : bond        0.04313 /  2.71 (  597)
  hydrogen bonds       : angle       4.33320 /  3.07 ( 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
  173 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 143
  time to evaluate  : 0.437 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.8003 (mt) cc_final: 0.7755 (tp)
REVERT: A   69 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7514 (mp0)
REVERT: A  128 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6281 (pm20)
REVERT: A  159 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8219 (tm-30)
REVERT: A  292 TRP cc_start: 0.7130 (m100) cc_final: 0.6466 (m-10)
REVERT: B   69 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7546 (mp0)
REVERT: B  128 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6761 (mp0)
REVERT: B  159 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8165 (tm-30)
REVERT: B  182 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6488 (mt-10)
REVERT: B  266 GLU cc_start: 0.7330 (tt0) cc_final: 0.7017 (tp30)
REVERT: B  477 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7567 (tp)
REVERT: C   69 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7639 (mp0)
REVERT: C  128 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6924 (mp0)
REVERT: C  159 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8209 (tm-30)
REVERT: C  292 TRP cc_start: 0.7105 (m100) cc_final: 0.6342 (m-10)
  outliers start: 30
  outliers final: 14
  residues processed: 165
  average time/residue: 0.4223
  time to fit residues: 78.1511
Evaluate side-chains
  157 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 135
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
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   63 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  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   69 GLU
Chi-restraints excluded: chain C residue  128 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
Chi-restraints excluded: chain C residue  499 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:    2.9990
   chunk 140 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 115 optimal weight:    0.1980
   chunk 10 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0070
   chunk 70 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 45 optimal weight:    7.9990
   chunk 137 optimal weight:    0.5980
   overall best weight:    0.5398

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.188851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.162376 restraints weight = 13389.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3806 rms_B_bonded: 1.94
r_work: 0.3581 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3629
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3629 r_free = 0.3629    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3629 r_free = 0.3629    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3629
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.3845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12267  Z= 0.112
  Angle     :  0.610   7.853  16656  Z= 0.304
  Chirality :  0.042   0.185   1908
  Planarity :  0.004   0.043   2013
  Dihedral  :  7.757  71.105   1659
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 19.39 %
    Favored  : 78.85 %
  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: -0.52 (0.23), residues: 1392
  helix:  0.60 (0.17), residues: 942
  sheet: -3.99 (0.67), residues: 30
  loop : -2.18 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 462 
 TYR   0.013   0.001   TYR C 177 
 PHE   0.029   0.001   PHE C 298 
 TRP   0.011   0.001   TRP B 257 
 HIS   0.004   0.001   HIS B 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.11 (12267)
  covalent geometry    : angle       0.60955 /  0.30 (16656)
  hydrogen bonds       : bond        0.03666 /  2.33 (  597)
  hydrogen bonds       : angle       4.13457 /  2.92 ( 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
  165 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 0.531 
Fit side-chains
REVERT: A   69 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7358 (mp0)
REVERT: A  128 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6279 (pm20)
REVERT: A  159 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8123 (tm-30)
REVERT: A  188 VAL cc_start: 0.7605 (p) cc_final: 0.7024 (t)
REVERT: A  292 TRP cc_start: 0.6906 (m100) cc_final: 0.6219 (m-10)
REVERT: B   69 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7454 (mp0)
REVERT: B  128 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.5890 (pm20)
REVERT: B  159 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8120 (tm-30)
REVERT: B  188 VAL cc_start: 0.7240 (p) cc_final: 0.6780 (t)
REVERT: B  266 GLU cc_start: 0.7254 (tt0) cc_final: 0.7034 (tp30)
REVERT: B  422 ARG cc_start: 0.7744 (mmt-90) cc_final: 0.7500 (mmt180)
REVERT: B  477 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7442 (tp)
REVERT: C   69 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7499 (mp0)
REVERT: C  128 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6972 (mp0)
REVERT: C  159 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8173 (tm-30)
REVERT: C  292 TRP cc_start: 0.6955 (m100) cc_final: 0.6357 (m-10)
REVERT: C  439 ARG cc_start: 0.7478 (ptp90) cc_final: 0.7261 (ptt90)
  outliers start: 22
  outliers final: 13
  residues processed: 159
  average time/residue: 0.4212
  time to fit residues: 74.9838
Evaluate side-chains
  150 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
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  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   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  408 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 106 optimal weight:    0.9980
   chunk 131 optimal weight:    5.9990
   chunk 15 optimal weight:    6.9990
   chunk 93 optimal weight:    0.0370
   chunk 4 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 134 optimal weight:    3.9990
   chunk 101 optimal weight:    0.0020
   overall best weight:    0.5868

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.185441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.157931 restraints weight = 13437.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 2.15
r_work: 0.3516 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3545
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3545 r_free = 0.3545    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3545 r_free = 0.3545    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (20 function evaluations)
r_final: 0.3545
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.3936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  12267  Z= 0.112
  Angle     :  0.604   6.472  16656  Z= 0.300
  Chirality :  0.042   0.182   1908
  Planarity :  0.004   0.040   2013
  Dihedral  :  7.623  71.982   1659
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 19.63 %
    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: -0.26 (0.23), residues: 1392
  helix:  0.77 (0.17), residues: 945
  sheet: -3.99 (0.66), residues: 30
  loop : -2.02 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 462 
 TYR   0.013   0.001   TYR C 177 
 PHE   0.030   0.001   PHE C 298 
 TRP   0.010   0.001   TRP C 180 
 HIS   0.007   0.001   HIS C 145 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00242 /  0.11 (12267)
  covalent geometry    : angle       0.60426 /  0.30 (16656)
  hydrogen bonds       : bond        0.03654 /  2.32 (  597)
  hydrogen bonds       : angle       4.11750 /  2.91 ( 1755)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3559.27 seconds
wall clock time: 61 minutes 37.43 seconds (3697.43 seconds total)