Starting phenix.real_space_refine
on Thu Sep 18 07:58:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ekw_48139/09_2025/9ekw_48139_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ekw_48139/09_2025/9ekw_48139.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ekw_48139/09_2025/9ekw_48139.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ekw_48139/09_2025/9ekw_48139.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ekw_48139/09_2025/9ekw_48139_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ekw_48139/09_2025/9ekw_48139_neut.cif"
  }
  resolution = 3.01
  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=   0.002 sd=   0.016
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      84      5.16       5
     C    9956      2.51       5
     N    2428      2.21       5
     O    2720      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15188
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3797
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 467, 3797
          Classifications: {'peptide': 467}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 8, 'TRANS': 458}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 12
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 3.08, per 1000 atoms: 0.20
  Number of scatterers: 15188
  At special positions: 0
  Unit cell: (115.866, 115.866, 118.08, 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      84     16.00
     O    2720      8.00
     N    2428      7.00
     C    9956      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 164 " - pdb=" SG  CYS A 190 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 164 " - pdb=" SG  CYS B 190 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 164 " - pdb=" SG  CYS C 190 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 164 " - pdb=" SG  CYS D 190 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.20
  Conformation dependent library (CDL) restraints added in 511.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3688 Ramachandran restraints generated.
    1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3552

  Finding SS restraints...
    Secondary structure from input PDB file:
      76 helices and 8 sheets defined
      67.1% alpha, 18.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 50
    Processing helix  chain 'A' and resid 51 through 56
    Processing helix  chain 'A' and resid 63 through 106
      removed outlier: 4.030A  pdb=" N   GLN A  69 " --> pdb=" O   LYS A  65 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   VAL A  74 " --> pdb=" O   ILE A  70 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   LEU A  89 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   VAL A  90 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 140
      removed outlier: 3.649A  pdb=" N   TYR A 128 " --> pdb=" O   GLN A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 145
    Processing helix  chain 'A' and resid 195 through 199
    Processing helix  chain 'A' and resid 203 through 212
      removed outlier: 6.256A  pdb=" N   SER A 209 " --> pdb=" O   LYS A 206 " (cutoff:3.500A)
      removed outlier: 5.997A  pdb=" N   PHE A 210 " --> pdb=" O   ASN A 207 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   PHE A 211 " --> pdb=" O   SER A 208 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ARG A 212 " --> pdb=" O   SER A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 238
      removed outlier: 3.865A  pdb=" N   HIS A 236 " --> pdb=" O   GLN A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 326
      removed outlier: 4.085A  pdb=" N   PHE A 326 " --> pdb=" O   PHE A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 371
      removed outlier: 3.745A  pdb=" N   LEU A 349 " --> pdb=" O   GLY A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 392
    Processing helix  chain 'A' and resid 393 through 398
      removed outlier: 3.651A  pdb=" N   LEU A 397 " --> pdb=" O   VAL A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 401
      No H-bonds generated for 'chain 'A' and resid 399 through 401'
    Processing helix  chain 'A' and resid 403 through 440
      removed outlier: 3.800A  pdb=" N   LEU A 414 " --> pdb=" O   MET A 410 " (cutoff:3.500A)
      Proline residue:  A 415  - end of helix
      removed outlier: 4.383A  pdb=" N   ARG A 419 " --> pdb=" O   PRO A 415 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ALA A 422 " --> pdb=" O   LEU A 418 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   CYS A 423 " --> pdb=" O   ARG A 419 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ILE A 427 " --> pdb=" O   CYS A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 447
      removed outlier: 6.956A  pdb=" N   ASP A 444 " --> pdb=" O   PRO A 441 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   LYS A 445 " --> pdb=" O   TYR A 442 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLU A 447 " --> pdb=" O   ASP A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 461
    Processing helix  chain 'A' and resid 464 through 471
      removed outlier: 3.665A  pdb=" N   THR A 468 " --> pdb=" O   ASP A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 497
      removed outlier: 3.610A  pdb=" N   MET A 497 " --> pdb=" O   LEU A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 520
      removed outlier: 3.552A  pdb=" N   PHE A 502 " --> pdb=" O   ILE A 498 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ILE A 503 " --> pdb=" O   LEU A 499 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 50
    Processing helix  chain 'B' and resid 51 through 56
    Processing helix  chain 'B' and resid 63 through 106
      removed outlier: 4.029A  pdb=" N   GLN B  69 " --> pdb=" O   LYS B  65 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   VAL B  74 " --> pdb=" O   ILE B  70 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   LEU B  89 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   VAL B  90 " --> pdb=" O   SER B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 140
      removed outlier: 3.649A  pdb=" N   TYR B 128 " --> pdb=" O   GLN B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 145
    Processing helix  chain 'B' and resid 195 through 199
    Processing helix  chain 'B' and resid 203 through 212
      removed outlier: 6.255A  pdb=" N   SER B 209 " --> pdb=" O   LYS B 206 " (cutoff:3.500A)
      removed outlier: 5.997A  pdb=" N   PHE B 210 " --> pdb=" O   ASN B 207 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   PHE B 211 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ARG B 212 " --> pdb=" O   SER B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 238
      removed outlier: 3.865A  pdb=" N   HIS B 236 " --> pdb=" O   GLN B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 326
      removed outlier: 4.085A  pdb=" N   PHE B 326 " --> pdb=" O   PHE B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 371
      removed outlier: 3.744A  pdb=" N   LEU B 349 " --> pdb=" O   GLY B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 375 through 392
    Processing helix  chain 'B' and resid 393 through 398
      removed outlier: 3.650A  pdb=" N   LEU B 397 " --> pdb=" O   VAL B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 401
      No H-bonds generated for 'chain 'B' and resid 399 through 401'
    Processing helix  chain 'B' and resid 403 through 440
      removed outlier: 3.800A  pdb=" N   LEU B 414 " --> pdb=" O   MET B 410 " (cutoff:3.500A)
      Proline residue:  B 415  - end of helix
      removed outlier: 4.383A  pdb=" N   ARG B 419 " --> pdb=" O   PRO B 415 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ALA B 422 " --> pdb=" O   LEU B 418 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   CYS B 423 " --> pdb=" O   ARG B 419 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ILE B 427 " --> pdb=" O   CYS B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 447
      removed outlier: 6.956A  pdb=" N   ASP B 444 " --> pdb=" O   PRO B 441 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   LYS B 445 " --> pdb=" O   TYR B 442 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   GLU B 447 " --> pdb=" O   ASP B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 461
    Processing helix  chain 'B' and resid 464 through 471
      removed outlier: 3.665A  pdb=" N   THR B 468 " --> pdb=" O   ASP B 464 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 497
      removed outlier: 3.610A  pdb=" N   MET B 497 " --> pdb=" O   LEU B 493 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 497 through 520
      removed outlier: 3.551A  pdb=" N   PHE B 502 " --> pdb=" O   ILE B 498 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ILE B 503 " --> pdb=" O   LEU B 499 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 50
    Processing helix  chain 'C' and resid 51 through 56
    Processing helix  chain 'C' and resid 63 through 106
      removed outlier: 4.030A  pdb=" N   GLN C  69 " --> pdb=" O   LYS C  65 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   VAL C  74 " --> pdb=" O   ILE C  70 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   LEU C  89 " --> pdb=" O   LEU C  85 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   VAL C  90 " --> pdb=" O   SER C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 123 through 140
      removed outlier: 3.649A  pdb=" N   TYR C 128 " --> pdb=" O   GLN C 124 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 145
    Processing helix  chain 'C' and resid 195 through 199
    Processing helix  chain 'C' and resid 203 through 212
      removed outlier: 6.255A  pdb=" N   SER C 209 " --> pdb=" O   LYS C 206 " (cutoff:3.500A)
      removed outlier: 5.997A  pdb=" N   PHE C 210 " --> pdb=" O   ASN C 207 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   PHE C 211 " --> pdb=" O   SER C 208 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ARG C 212 " --> pdb=" O   SER C 209 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 232 through 238
      removed outlier: 3.865A  pdb=" N   HIS C 236 " --> pdb=" O   GLN C 233 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 326
      removed outlier: 4.085A  pdb=" N   PHE C 326 " --> pdb=" O   PHE C 322 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 345 through 371
      removed outlier: 3.745A  pdb=" N   LEU C 349 " --> pdb=" O   GLY C 345 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 375 through 392
    Processing helix  chain 'C' and resid 393 through 398
      removed outlier: 3.651A  pdb=" N   LEU C 397 " --> pdb=" O   VAL C 393 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 399 through 401
      No H-bonds generated for 'chain 'C' and resid 399 through 401'
    Processing helix  chain 'C' and resid 403 through 440
      removed outlier: 3.801A  pdb=" N   LEU C 414 " --> pdb=" O   MET C 410 " (cutoff:3.500A)
      Proline residue:  C 415  - end of helix
      removed outlier: 4.383A  pdb=" N   ARG C 419 " --> pdb=" O   PRO C 415 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ALA C 422 " --> pdb=" O   LEU C 418 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   CYS C 423 " --> pdb=" O   ARG C 419 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ILE C 427 " --> pdb=" O   CYS C 423 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 441 through 447
      removed outlier: 6.956A  pdb=" N   ASP C 444 " --> pdb=" O   PRO C 441 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   LYS C 445 " --> pdb=" O   TYR C 442 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   GLU C 447 " --> pdb=" O   ASP C 444 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 448 through 461
    Processing helix  chain 'C' and resid 464 through 471
      removed outlier: 3.665A  pdb=" N   THR C 468 " --> pdb=" O   ASP C 464 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 476 through 497
      removed outlier: 3.610A  pdb=" N   MET C 497 " --> pdb=" O   LEU C 493 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 497 through 520
      removed outlier: 3.552A  pdb=" N   PHE C 502 " --> pdb=" O   ILE C 498 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ILE C 503 " --> pdb=" O   LEU C 499 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 42 through 50
    Processing helix  chain 'D' and resid 51 through 56
    Processing helix  chain 'D' and resid 63 through 106
      removed outlier: 4.030A  pdb=" N   GLN D  69 " --> pdb=" O   LYS D  65 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   VAL D  74 " --> pdb=" O   ILE D  70 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   LEU D  89 " --> pdb=" O   LEU D  85 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   VAL D  90 " --> pdb=" O   SER D  86 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 140
      removed outlier: 3.649A  pdb=" N   TYR D 128 " --> pdb=" O   GLN D 124 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 140 through 145
    Processing helix  chain 'D' and resid 195 through 199
    Processing helix  chain 'D' and resid 203 through 212
      removed outlier: 6.257A  pdb=" N   SER D 209 " --> pdb=" O   LYS D 206 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   PHE D 210 " --> pdb=" O   ASN D 207 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   PHE D 211 " --> pdb=" O   SER D 208 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ARG D 212 " --> pdb=" O   SER D 209 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 232 through 238
      removed outlier: 3.865A  pdb=" N   HIS D 236 " --> pdb=" O   GLN D 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 326
      removed outlier: 4.085A  pdb=" N   PHE D 326 " --> pdb=" O   PHE D 322 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 345 through 371
      removed outlier: 3.745A  pdb=" N   LEU D 349 " --> pdb=" O   GLY D 345 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 375 through 392
    Processing helix  chain 'D' and resid 393 through 398
      removed outlier: 3.651A  pdb=" N   LEU D 397 " --> pdb=" O   VAL D 393 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 399 through 401
      No H-bonds generated for 'chain 'D' and resid 399 through 401'
    Processing helix  chain 'D' and resid 403 through 440
      removed outlier: 3.800A  pdb=" N   LEU D 414 " --> pdb=" O   MET D 410 " (cutoff:3.500A)
      Proline residue:  D 415  - end of helix
      removed outlier: 4.383A  pdb=" N   ARG D 419 " --> pdb=" O   PRO D 415 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ALA D 422 " --> pdb=" O   LEU D 418 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   CYS D 423 " --> pdb=" O   ARG D 419 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ILE D 427 " --> pdb=" O   CYS D 423 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 441 through 447
      removed outlier: 6.956A  pdb=" N   ASP D 444 " --> pdb=" O   PRO D 441 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   LYS D 445 " --> pdb=" O   TYR D 442 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLU D 447 " --> pdb=" O   ASP D 444 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 448 through 461
    Processing helix  chain 'D' and resid 464 through 471
      removed outlier: 3.665A  pdb=" N   THR D 468 " --> pdb=" O   ASP D 464 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 476 through 497
      removed outlier: 3.610A  pdb=" N   MET D 497 " --> pdb=" O   LEU D 493 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 497 through 520
      removed outlier: 3.552A  pdb=" N   PHE D 502 " --> pdb=" O   ILE D 498 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ILE D 503 " --> pdb=" O   LEU D 499 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 121
      removed outlier: 3.575A  pdb=" N   CYS A 119 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   HIS A 226 " --> pdb=" O   GLY A 152 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 121
      removed outlier: 3.575A  pdb=" N   CYS A 119 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   GLN A 166 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   VAL A 221 " --> pdb=" O   CYS A 164 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   CYS A 164 " --> pdb=" O   VAL A 221 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A 162 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   LYS A 162 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   PHE A 225 " --> pdb=" O   GLY A 160 " (cutoff:3.500A)
      removed outlier: 8.831A  pdb=" N   GLY A 160 " --> pdb=" O   PHE A 225 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 119 through 121
      removed outlier: 3.575A  pdb=" N   CYS B 119 " --> pdb=" O   ILE B 263 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   HIS B 226 " --> pdb=" O   GLY B 152 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 119 through 121
      removed outlier: 3.575A  pdb=" N   CYS B 119 " --> pdb=" O   ILE B 263 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   GLN B 166 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   VAL B 221 " --> pdb=" O   CYS B 164 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   CYS B 164 " --> pdb=" O   VAL B 221 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   ILE B 223 " --> pdb=" O   LYS B 162 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   LYS B 162 " --> pdb=" O   ILE B 223 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   PHE B 225 " --> pdb=" O   GLY B 160 " (cutoff:3.500A)
      removed outlier: 8.831A  pdb=" N   GLY B 160 " --> pdb=" O   PHE B 225 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 119 through 121
      removed outlier: 3.575A  pdb=" N   CYS C 119 " --> pdb=" O   ILE C 263 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   HIS C 226 " --> pdb=" O   GLY C 152 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 119 through 121
      removed outlier: 3.575A  pdb=" N   CYS C 119 " --> pdb=" O   ILE C 263 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   GLN C 166 " --> pdb=" O   LEU C 219 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   VAL C 221 " --> pdb=" O   CYS C 164 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   CYS C 164 " --> pdb=" O   VAL C 221 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   ILE C 223 " --> pdb=" O   LYS C 162 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   LYS C 162 " --> pdb=" O   ILE C 223 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   PHE C 225 " --> pdb=" O   GLY C 160 " (cutoff:3.500A)
      removed outlier: 8.832A  pdb=" N   GLY C 160 " --> pdb=" O   PHE C 225 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 119 through 121
      removed outlier: 3.574A  pdb=" N   CYS D 119 " --> pdb=" O   ILE D 263 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   HIS D 226 " --> pdb=" O   GLY D 152 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 119 through 121
      removed outlier: 3.574A  pdb=" N   CYS D 119 " --> pdb=" O   ILE D 263 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   GLN D 166 " --> pdb=" O   LEU D 219 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   VAL D 221 " --> pdb=" O   CYS D 164 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   CYS D 164 " --> pdb=" O   VAL D 221 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   ILE D 223 " --> pdb=" O   LYS D 162 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   LYS D 162 " --> pdb=" O   ILE D 223 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   PHE D 225 " --> pdb=" O   GLY D 160 " (cutoff:3.500A)
      removed outlier: 8.831A  pdb=" N   GLY D 160 " --> pdb=" O   PHE D 225 " (cutoff:3.500A)

    1085 hydrogen bonds defined for protein.
    3135 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: 2.54

  Time building geometry restraints manager: 1.63 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3182
        1.33 -     1.45: 3671
        1.45 -     1.57: 8563
        1.57 -     1.69: 0
        1.69 -     1.81: 116
  Bond restraints: 15532
  Sorted by residual:
  bond pdb=" CE1 HIS D 167 "
       pdb=" NE2 HIS D 167 "
    ideal  model  delta    sigma   weight residual
    1.321  1.359 -0.038 1.00e-02 1.00e+04 1.43e+01
  bond pdb=" CE1 HIS A 167 "
       pdb=" NE2 HIS A 167 "
    ideal  model  delta    sigma   weight residual
    1.321  1.359 -0.038 1.00e-02 1.00e+04 1.41e+01
  bond pdb=" CE1 HIS C 167 "
       pdb=" NE2 HIS C 167 "
    ideal  model  delta    sigma   weight residual
    1.321  1.358 -0.037 1.00e-02 1.00e+04 1.40e+01
  bond pdb=" CE1 HIS B 167 "
       pdb=" NE2 HIS B 167 "
    ideal  model  delta    sigma   weight residual
    1.321  1.358 -0.037 1.00e-02 1.00e+04 1.38e+01
  bond pdb=" N   ILE A 513 "
       pdb=" CA  ILE A 513 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.035 1.19e-02 7.06e+03 8.51e+00
  ... (remaining 15527 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 19520
        1.52 -     3.05: 1185
        3.05 -     4.57: 247
        4.57 -     6.10: 36
        6.10 -     7.62: 24
  Bond angle restraints: 21012
  Sorted by residual:
  angle pdb=" C   LYS D 200 "
        pdb=" CA  LYS D 200 "
        pdb=" CB  LYS D 200 "
      ideal   model   delta    sigma   weight residual
     109.71  117.33   -7.62 1.39e+00 5.18e-01 3.01e+01
  angle pdb=" C   LYS C 200 "
        pdb=" CA  LYS C 200 "
        pdb=" CB  LYS C 200 "
      ideal   model   delta    sigma   weight residual
     109.71  117.33   -7.62 1.39e+00 5.18e-01 3.00e+01
  angle pdb=" C   LYS A 200 "
        pdb=" CA  LYS A 200 "
        pdb=" CB  LYS A 200 "
      ideal   model   delta    sigma   weight residual
     109.71  117.32   -7.61 1.39e+00 5.18e-01 3.00e+01
  angle pdb=" C   LYS B 200 "
        pdb=" CA  LYS B 200 "
        pdb=" CB  LYS B 200 "
      ideal   model   delta    sigma   weight residual
     109.71  117.31   -7.60 1.39e+00 5.18e-01 2.99e+01
  angle pdb=" N   LYS C 200 "
        pdb=" CA  LYS C 200 "
        pdb=" C   LYS C 200 "
      ideal   model   delta    sigma   weight residual
     110.42  102.88    7.54 1.46e+00 4.69e-01 2.67e+01
  ... (remaining 21007 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.49: 8215
       16.49 -    32.98: 710
       32.98 -    49.47: 159
       49.47 -    65.96: 32
       65.96 -    82.45: 12
  Dihedral angle restraints: 9128
    sinusoidal: 3620
      harmonic: 5508
  Sorted by residual:
  dihedral pdb=" CA  ASP B 183 "
           pdb=" C   ASP B 183 "
           pdb=" N   ASN B 184 "
           pdb=" CA  ASN B 184 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.94   29.06     0      5.00e+00 4.00e-02 3.38e+01
  dihedral pdb=" CA  ASP A 183 "
           pdb=" C   ASP A 183 "
           pdb=" N   ASN A 184 "
           pdb=" CA  ASN A 184 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.97   29.03     0      5.00e+00 4.00e-02 3.37e+01
  dihedral pdb=" CA  ASP C 183 "
           pdb=" C   ASP C 183 "
           pdb=" N   ASN C 184 "
           pdb=" CA  ASN C 184 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.97   29.03     0      5.00e+00 4.00e-02 3.37e+01
  ... (remaining 9125 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1841
       0.056 -    0.112: 408
       0.112 -    0.167: 119
       0.167 -    0.223: 4
       0.223 -    0.279: 4
  Chirality restraints: 2376
  Sorted by residual:
  chirality pdb=" CA  ILE A 279 "
            pdb=" N   ILE A 279 "
            pdb=" C   ILE A 279 "
            pdb=" CB  ILE A 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.28 2.00e-01 2.50e+01 1.95e+00
  chirality pdb=" CA  ILE C 279 "
            pdb=" N   ILE C 279 "
            pdb=" C   ILE C 279 "
            pdb=" CB  ILE C 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" CA  ILE D 279 "
            pdb=" N   ILE D 279 "
            pdb=" C   ILE D 279 "
            pdb=" CB  ILE D 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.28 2.00e-01 2.50e+01 1.93e+00
  ... (remaining 2373 not shown)

  Planarity restraints: 2604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 197 "    0.013 2.00e-02 2.50e+03   2.58e-02 6.65e+00
        pdb=" C   ASP A 197 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   ASP A 197 "    0.017 2.00e-02 2.50e+03
        pdb=" N   LEU A 198 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 197 "    0.013 2.00e-02 2.50e+03   2.58e-02 6.64e+00
        pdb=" C   ASP B 197 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   ASP B 197 "    0.017 2.00e-02 2.50e+03
        pdb=" N   LEU B 198 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP D 197 "   -0.013 2.00e-02 2.50e+03   2.57e-02 6.60e+00
        pdb=" C   ASP D 197 "    0.044 2.00e-02 2.50e+03
        pdb=" O   ASP D 197 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   LEU D 198 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 2601 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 107
        2.58 -     3.16: 12939
        3.16 -     3.74: 22491
        3.74 -     4.32: 31843
        4.32 -     4.90: 53720
  Nonbonded interactions: 121100
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 357 "
            pdb=" OG  SER A 385 "
     model   vdw
     2.000 3.040
  nonbonded pdb=" OG1 THR C 357 "
            pdb=" OG  SER C 385 "
     model   vdw
     2.000 3.040
  nonbonded pdb=" OG1 THR D 357 "
            pdb=" OG  SER D 385 "
     model   vdw
     2.000 3.040
  nonbonded pdb=" OG1 THR B 357 "
            pdb=" OG  SER B 385 "
     model   vdw
     2.001 3.040
  nonbonded pdb=" N   GLN D 196 "
            pdb=" OE1 GLN D 196 "
     model   vdw
     2.192 3.120
  ... (remaining 121095 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.750
  Find NCS groups from input model:        0.120
  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:0.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  15536  Z= 0.343
  Angle     :  0.853   7.624  21020  Z= 0.557
  Chirality :  0.052   0.279   2376
  Planarity :  0.005   0.058   2604
  Dihedral  : 13.440  82.450   5564
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  8.39 %
    Favored  : 91.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.19), residues: 1844
  helix:  1.13 (0.15), residues: 1088
  sheet:  1.16 (0.33), residues: 196
  loop : -1.10 (0.25), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 484 
 TYR   0.021   0.002   TYR D  48 
 PHE   0.017   0.002   PHE A 381 
 TRP   0.018   0.002   TRP A  64 
 HIS   0.005   0.002   HIS C 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 (15532)
  covalent geometry    : angle       0.85299 (21012)
  SS BOND              : bond        0.00210 (    4)
  SS BOND              : angle       0.80308 (    8)
  hydrogen bonds       : bond        0.14974 (  993)
  hydrogen bonds       : angle       6.50672 ( 3135)

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

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

  3688 Ramachandran restraints generated.
    1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3688 Ramachandran restraints generated.
    1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 237
  time to evaluate  : 0.594 
Fit side-chains
REVERT: A   50 MET cc_start: 0.7974 (ptp) cc_final: 0.7771 (ptp)
REVERT: A   54 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7023 (mm-30)
REVERT: A  187 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7331 (mt-10)
REVERT: A  222 GLU cc_start: 0.8412 (tt0) cc_final: 0.7835 (pt0)
REVERT: A  374 ASN cc_start: 0.7928 (t0) cc_final: 0.7726 (t0)
REVERT: B   50 MET cc_start: 0.8118 (ptp) cc_final: 0.7891 (ptp)
REVERT: B   54 GLU cc_start: 0.7569 (mm-30) cc_final: 0.6989 (mm-30)
REVERT: B  187 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7309 (mt-10)
REVERT: B  222 GLU cc_start: 0.8421 (tt0) cc_final: 0.7845 (pt0)
REVERT: B  497 MET cc_start: 0.5882 (ttm) cc_final: 0.5674 (mtt)
REVERT: C   50 MET cc_start: 0.8107 (ptp) cc_final: 0.7881 (ptp)
REVERT: C   54 GLU cc_start: 0.7564 (mm-30) cc_final: 0.6981 (mm-30)
REVERT: C  187 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7122 (mt-10)
REVERT: C  222 GLU cc_start: 0.8415 (tt0) cc_final: 0.7815 (pt0)
REVERT: D   50 MET cc_start: 0.8069 (ptp) cc_final: 0.7828 (ptp)
REVERT: D  187 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7314 (mt-10)
REVERT: D  222 GLU cc_start: 0.8418 (tt0) cc_final: 0.7864 (pt0)
REVERT: D  497 MET cc_start: 0.5988 (ttm) cc_final: 0.5737 (mtt)
  outliers start: 8
  outliers final: 0
  residues processed: 245
  average time/residue: 0.1445
  time to fit residues: 49.9966
Evaluate side-chains
  190 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    4.9990
   chunk 149 optimal weight:    6.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 247 GLN
A 471 GLN
B 184 ASN
** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 471 GLN
** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 401 GLN
C 471 GLN
** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 471 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.151677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.102447 restraints weight = 19929.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.71
r_work: 0.3071 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  15536  Z= 0.209
  Angle     :  0.603   5.738  21020  Z= 0.334
  Chirality :  0.042   0.145   2376
  Planarity :  0.004   0.043   2604
  Dihedral  :  4.993  27.461   2016
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  :  8.39 %
    Favored  : 89.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.46 (0.19), residues: 1844
  helix:  2.00 (0.15), residues: 1096
  sheet:  1.58 (0.33), residues: 196
  loop : -1.47 (0.24), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  57 
 TYR   0.015   0.002   TYR B 486 
 PHE   0.012   0.001   PHE B 469 
 TRP   0.012   0.002   TRP D 390 
 HIS   0.008   0.001   HIS B 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 (15532)
  covalent geometry    : angle       0.60329 (21012)
  SS BOND              : bond        0.00031 (    4)
  SS BOND              : angle       0.19849 (    8)
  hydrogen bonds       : bond        0.05066 (  993)
  hydrogen bonds       : angle       4.49971 ( 3135)

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

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

  3688 Ramachandran restraints generated.
    1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3688 Ramachandran restraints generated.
    1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 180
  time to evaluate  : 0.615 
Fit side-chains
REVERT: A   54 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7116 (mm-30)
REVERT: A  187 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7318 (mt-10)
REVERT: A  222 GLU cc_start: 0.8550 (tt0) cc_final: 0.7933 (pt0)
REVERT: A  366 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6898 (tp30)
REVERT: A  372 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7225 (mp)
REVERT: A  373 THR cc_start: 0.7975 (p) cc_final: 0.7692 (m)
REVERT: B   54 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7128 (mm-30)
REVERT: B  187 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7349 (mt-10)
REVERT: B  200 LYS cc_start: 0.8462 (ttpt) cc_final: 0.8183 (tttm)
REVERT: B  222 GLU cc_start: 0.8578 (tt0) cc_final: 0.7942 (pt0)
REVERT: B  366 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6919 (tp30)
REVERT: B  372 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7332 (mp)
REVERT: B  497 MET cc_start: 0.6256 (ttm) cc_final: 0.5970 (mtt)
REVERT: C   54 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7122 (mm-30)
REVERT: C  169 LYS cc_start: 0.8240 (ttmt) cc_final: 0.7901 (ttpt)
REVERT: C  187 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7354 (mt-10)
REVERT: C  200 LYS cc_start: 0.8465 (ttpt) cc_final: 0.8187 (tttm)
REVERT: C  222 GLU cc_start: 0.8584 (tt0) cc_final: 0.7947 (pt0)
REVERT: C  366 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6896 (tp30)
REVERT: C  372 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7317 (mp)
REVERT: D   54 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7087 (mm-30)
REVERT: D  187 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7325 (mt-10)
REVERT: D  200 LYS cc_start: 0.8410 (ttpt) cc_final: 0.8139 (tttm)
REVERT: D  222 GLU cc_start: 0.8563 (tt0) cc_final: 0.7948 (pt0)
REVERT: D  366 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6902 (tp30)
REVERT: D  372 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7281 (mp)
REVERT: D  497 MET cc_start: 0.6296 (ttm) cc_final: 0.5963 (mtt)
  outliers start: 36
  outliers final: 17
  residues processed: 202
  average time/residue: 0.1223
  time to fit residues: 37.0436
Evaluate side-chains
  191 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 166
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  366 GLU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  516 PHE
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  189 ASP
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  366 GLU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  516 PHE
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  189 ASP
Chi-restraints excluded: chain C residue  268 ASP
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  366 GLU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  516 PHE
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  189 ASP
Chi-restraints excluded: chain D residue  268 ASP
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  366 GLU
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  516 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 74 optimal weight:   20.0000
   chunk 11 optimal weight:    0.6980
   chunk 151 optimal weight:    8.9990
   chunk 179 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 180 optimal weight:    1.9990
   chunk 174 optimal weight:    0.8980
   chunk 161 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
B 184 ASN
B 247 GLN
B 401 GLN
** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 247 GLN
** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 247 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.158397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.109029 restraints weight = 20049.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 2.94
r_work: 0.3277 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  15536  Z= 0.123
  Angle     :  0.494   4.957  21020  Z= 0.274
  Chirality :  0.038   0.135   2376
  Planarity :  0.004   0.042   2604
  Dihedral  :  4.471  21.979   2016
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  :  8.87 %
    Favored  : 89.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.09 (0.20), residues: 1844
  helix:  2.45 (0.16), residues: 1096
  sheet:  1.79 (0.33), residues: 196
  loop : -1.07 (0.26), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  57 
 TYR   0.019   0.001   TYR B  48 
 PHE   0.011   0.001   PHE D 225 
 TRP   0.008   0.001   TRP A 390 
 HIS   0.005   0.001   HIS C 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (15532)
  covalent geometry    : angle       0.49362 (21012)
  SS BOND              : bond        0.00002 (    4)
  SS BOND              : angle       0.15508 (    8)
  hydrogen bonds       : bond        0.04139 (  993)
  hydrogen bonds       : angle       4.05277 ( 3135)

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

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

  3688 Ramachandran restraints generated.
    1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3688 Ramachandran restraints generated.
    1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 177
  time to evaluate  : 0.583 
Fit side-chains
REVERT: A  187 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7351 (mt-10)
REVERT: A  222 GLU cc_start: 0.8497 (tt0) cc_final: 0.7968 (pt0)
REVERT: A  366 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6828 (tp30)
REVERT: B  187 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7298 (mt-10)
REVERT: B  222 GLU cc_start: 0.8510 (tt0) cc_final: 0.7957 (pt0)
REVERT: B  366 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6811 (tp30)
REVERT: C  169 LYS cc_start: 0.8358 (ttmt) cc_final: 0.8029 (ttpt)
REVERT: C  187 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7195 (mt-10)
REVERT: C  222 GLU cc_start: 0.8507 (tt0) cc_final: 0.7963 (pt0)
REVERT: C  366 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6819 (tp30)
REVERT: D  187 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7291 (mt-10)
REVERT: D  222 GLU cc_start: 0.8509 (tt0) cc_final: 0.7972 (pt0)
REVERT: D  366 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6819 (tp30)
REVERT: D  497 MET cc_start: 0.5935 (ttm) cc_final: 0.5716 (mtt)
  outliers start: 35
  outliers final: 18
  residues processed: 194
  average time/residue: 0.1166
  time to fit residues: 34.6222
Evaluate side-chains
  185 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 163
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  189 ASP
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  366 GLU
Chi-restraints excluded: chain A residue  516 PHE
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  268 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  366 GLU
Chi-restraints excluded: chain B residue  516 PHE
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  366 GLU
Chi-restraints excluded: chain C residue  516 PHE
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  366 GLU
Chi-restraints excluded: chain D residue  516 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 107 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 175 optimal weight:    3.9990
   chunk 179 optimal weight:    0.5980
   chunk 162 optimal weight:    6.9990
   chunk 101 optimal weight:    0.5980
   chunk 142 optimal weight:    3.9990
   chunk 116 optimal weight:    6.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.157943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.109348 restraints weight = 19836.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.85
r_work: 0.3271 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.2625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  15536  Z= 0.128
  Angle     :  0.487   4.931  21020  Z= 0.268
  Chirality :  0.038   0.134   2376
  Planarity :  0.003   0.039   2604
  Dihedral  :  4.247  19.604   2016
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 10.31 %
    Favored  : 87.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.17 (0.20), residues: 1844
  helix:  2.50 (0.15), residues: 1096
  sheet:  1.82 (0.33), residues: 196
  loop : -1.00 (0.27), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  57 
 TYR   0.019   0.001   TYR A  48 
 PHE   0.010   0.001   PHE C 225 
 TRP   0.007   0.001   TRP D 390 
 HIS   0.004   0.001   HIS C 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (15532)
  covalent geometry    : angle       0.48712 (21012)
  SS BOND              : bond        0.00032 (    4)
  SS BOND              : angle       0.18231 (    8)
  hydrogen bonds       : bond        0.04075 (  993)
  hydrogen bonds       : angle       3.93015 ( 3135)

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

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

  3688 Ramachandran restraints generated.
    1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3688 Ramachandran restraints generated.
    1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 170
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
REVERT: A  187 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7314 (mt-10)
REVERT: A  222 GLU cc_start: 0.8451 (tt0) cc_final: 0.8000 (pt0)
REVERT: A  366 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6802 (tp30)
REVERT: B  169 LYS cc_start: 0.8299 (ttpt) cc_final: 0.7935 (ttpt)
REVERT: B  187 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7364 (mt-10)
REVERT: B  222 GLU cc_start: 0.8455 (tt0) cc_final: 0.7990 (pt0)
REVERT: B  366 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6777 (tp30)
REVERT: B  372 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7485 (mp)
REVERT: C  187 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7353 (mt-10)
REVERT: C  222 GLU cc_start: 0.8472 (tt0) cc_final: 0.8014 (pt0)
REVERT: C  366 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6783 (tp30)
REVERT: C  372 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7440 (mp)
REVERT: D  187 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7351 (mt-10)
REVERT: D  222 GLU cc_start: 0.8449 (tt0) cc_final: 0.8004 (pt0)
REVERT: D  366 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6815 (tp30)
REVERT: D  372 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7440 (mp)
  outliers start: 34
  outliers final: 20
  residues processed: 189
  average time/residue: 0.1183
  time to fit residues: 34.1054
Evaluate side-chains
  195 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 168
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  366 GLU
Chi-restraints excluded: chain A residue  516 PHE
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  268 ASP
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  366 GLU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  516 PHE
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  366 GLU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  516 PHE
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  366 GLU
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  516 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 178 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 86 optimal weight:    0.6980
   chunk 172 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9990
   chunk 141 optimal weight:    0.2980
   chunk 53 optimal weight:    0.0370
   chunk 18 optimal weight:    5.9990
   chunk 122 optimal weight:    1.9990
   chunk 143 optimal weight:    0.8980
   overall best weight:    0.5860

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

Flipped N/Q/H residues before XYZ refinement:
A 167 HIS
** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 167 HIS
C 167 HIS
D 167 HIS
** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.160627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.111022 restraints weight = 19868.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 2.97
r_work: 0.3293 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.2972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  15536  Z= 0.100
  Angle     :  0.442   4.491  21020  Z= 0.244
  Chirality :  0.036   0.130   2376
  Planarity :  0.003   0.038   2604
  Dihedral  :  3.926  16.832   2016
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 11.27 %
    Favored  : 86.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.44 (0.20), residues: 1844
  helix:  2.69 (0.15), residues: 1096
  sheet:  1.33 (0.33), residues: 220
  loop : -0.67 (0.28), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  57 
 TYR   0.015   0.001   TYR A  48 
 PHE   0.011   0.001   PHE B 225 
 TRP   0.007   0.001   TRP C  64 
 HIS   0.003   0.000   HIS C 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 (15532)
  covalent geometry    : angle       0.44223 (21012)
  SS BOND              : bond        0.00029 (    4)
  SS BOND              : angle       0.08657 (    8)
  hydrogen bonds       : bond        0.03464 (  993)
  hydrogen bonds       : angle       3.71486 ( 3135)

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

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

  3688 Ramachandran restraints generated.
    1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3688 Ramachandran restraints generated.
    1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 190
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
REVERT: A  187 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7154 (mt-10)
REVERT: A  219 LEU cc_start: 0.7623 (mp) cc_final: 0.7369 (mp)
REVERT: A  222 GLU cc_start: 0.8417 (tt0) cc_final: 0.7966 (pt0)
REVERT: A  247 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7846 (mm-40)
REVERT: A  273 GLU cc_start: 0.7874 (tt0) cc_final: 0.7616 (pp20)
REVERT: A  372 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7162 (mp)
REVERT: B  187 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7396 (pt0)
REVERT: B  222 GLU cc_start: 0.8425 (tt0) cc_final: 0.7963 (pt0)
REVERT: B  372 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7339 (mp)
REVERT: C  187 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7461 (pt0)
REVERT: C  219 LEU cc_start: 0.7610 (mp) cc_final: 0.7362 (mp)
REVERT: C  222 GLU cc_start: 0.8430 (tt0) cc_final: 0.7978 (pt0)
REVERT: D  183 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7830 (m-30)
REVERT: D  187 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7231 (mt-10)
REVERT: D  219 LEU cc_start: 0.7620 (mp) cc_final: 0.7372 (mp)
REVERT: D  222 GLU cc_start: 0.8404 (tt0) cc_final: 0.7965 (pt0)
REVERT: D  372 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7339 (mp)
  outliers start: 29
  outliers final: 20
  residues processed: 207
  average time/residue: 0.1184
  time to fit residues: 37.0912
Evaluate side-chains
  197 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 172
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  189 ASP
Chi-restraints excluded: chain A residue  247 GLN
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  516 PHE
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  516 PHE
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  516 PHE
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  183 ASP
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  516 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 116 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   chunk 136 optimal weight:    2.9990
   chunk 112 optimal weight:    5.9990
   chunk 121 optimal weight:    3.9990
   chunk 165 optimal weight:   20.0000
   chunk 106 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 59 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.153269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.103168 restraints weight = 19982.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 2.86
r_work: 0.3194 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.2876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032  15536  Z= 0.216
  Angle     :  0.561   6.610  21020  Z= 0.305
  Chirality :  0.040   0.176   2376
  Planarity :  0.003   0.036   2604
  Dihedral  :  4.278  17.691   2016
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 11.81 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.13 (0.20), residues: 1844
  helix:  2.47 (0.15), residues: 1088
  sheet:  1.63 (0.34), residues: 196
  loop : -0.88 (0.27), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 484 
 TYR   0.020   0.002   TYR A 486 
 PHE   0.010   0.001   PHE C 457 
 TRP   0.009   0.001   TRP D 390 
 HIS   0.005   0.001   HIS C 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00528 (15532)
  covalent geometry    : angle       0.56076 (21012)
  SS BOND              : bond        0.00086 (    4)
  SS BOND              : angle       0.43606 (    8)
  hydrogen bonds       : bond        0.04800 (  993)
  hydrogen bonds       : angle       4.06195 ( 3135)

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

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

  3688 Ramachandran restraints generated.
    1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3688 Ramachandran restraints generated.
    1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 164
  time to evaluate  : 0.530 
Fit side-chains
REVERT: A  183 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.7937 (m-30)
REVERT: A  187 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7204 (mt-10)
REVERT: A  200 LYS cc_start: 0.8187 (ttpt) cc_final: 0.7718 (tptp)
REVERT: A  222 GLU cc_start: 0.8437 (tt0) cc_final: 0.8038 (pt0)
REVERT: A  247 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7885 (mm-40)
REVERT: A  366 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6859 (tp30)
REVERT: A  372 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7629 (mp)
REVERT: A  426 MET cc_start: 0.8304 (mmp) cc_final: 0.8053 (mmp)
REVERT: B  183 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.7955 (m-30)
REVERT: B  187 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7413 (pt0)
REVERT: B  222 GLU cc_start: 0.8459 (tt0) cc_final: 0.8047 (pt0)
REVERT: B  366 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6819 (tp30)
REVERT: B  372 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7766 (mp)
REVERT: C  183 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.7971 (m-30)
REVERT: C  187 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7471 (pt0)
REVERT: C  222 GLU cc_start: 0.8455 (tt0) cc_final: 0.8052 (pt0)
REVERT: C  366 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6833 (tp30)
REVERT: C  372 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7703 (mp)
REVERT: C  426 MET cc_start: 0.8298 (mmp) cc_final: 0.8040 (mmp)
REVERT: D  183 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8018 (m-30)
REVERT: D  187 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7255 (mt-10)
REVERT: D  222 GLU cc_start: 0.8442 (tt0) cc_final: 0.8044 (pt0)
REVERT: D  366 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.5865 (mp0)
REVERT: D  372 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7702 (mp)
REVERT: D  426 MET cc_start: 0.8279 (mmp) cc_final: 0.8011 (mmp)
  outliers start: 43
  outliers final: 24
  residues processed: 193
  average time/residue: 0.1115
  time to fit residues: 32.7751
Evaluate side-chains
  197 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 160
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  189 ASP
Chi-restraints excluded: chain A residue  247 GLN
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  366 GLU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  516 PHE
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  183 ASP
Chi-restraints excluded: chain B residue  189 ASP
Chi-restraints excluded: chain B residue  268 ASP
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  366 GLU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  516 PHE
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  183 ASP
Chi-restraints excluded: chain C residue  189 ASP
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  366 GLU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  516 PHE
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  183 ASP
Chi-restraints excluded: chain D residue  189 ASP
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  366 GLU
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  516 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 144 optimal weight:    0.8980
   chunk 180 optimal weight:    0.9980
   chunk 175 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 123 optimal weight:    3.9990
   chunk 142 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 84 optimal weight:    2.9990
   chunk 126 optimal weight:    7.9990
   chunk 127 optimal weight:    1.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.156139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.106386 restraints weight = 19710.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 2.86
r_work: 0.3241 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.3026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  15536  Z= 0.133
  Angle     :  0.484   5.415  21020  Z= 0.267
  Chirality :  0.037   0.154   2376
  Planarity :  0.003   0.035   2604
  Dihedral  :  4.073  17.570   2016
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 12.29 %
    Favored  : 85.49 %
  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 aren not related in a simple way.
  whole:  2.22 (0.20), residues: 1844
  helix:  2.50 (0.15), residues: 1096
  sheet:  1.30 (0.33), residues: 216
  loop : -0.72 (0.28), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  57 
 TYR   0.015   0.001   TYR A 486 
 PHE   0.010   0.001   PHE C 225 
 TRP   0.007   0.001   TRP A 390 
 HIS   0.003   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (15532)
  covalent geometry    : angle       0.48395 (21012)
  SS BOND              : bond        0.00076 (    4)
  SS BOND              : angle       0.16035 (    8)
  hydrogen bonds       : bond        0.04031 (  993)
  hydrogen bonds       : angle       3.87593 ( 3135)

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

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

  3688 Ramachandran restraints generated.
    1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3688 Ramachandran restraints generated.
    1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 170
  time to evaluate  : 0.560 
Fit side-chains
REVERT: A   73 ILE cc_start: 0.7776 (mp) cc_final: 0.7527 (mp)
REVERT: A  183 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.7962 (m-30)
REVERT: A  187 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7234 (mt-10)
REVERT: A  200 LYS cc_start: 0.8171 (ttpt) cc_final: 0.7708 (tptp)
REVERT: A  219 LEU cc_start: 0.7804 (mp) cc_final: 0.7537 (mp)
REVERT: A  222 GLU cc_start: 0.8394 (tt0) cc_final: 0.8006 (pt0)
REVERT: A  247 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7951 (tp40)
REVERT: A  372 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7519 (mp)
REVERT: B   73 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7545 (mp)
REVERT: B  183 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.7999 (m-30)
REVERT: B  187 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7446 (pt0)
REVERT: B  222 GLU cc_start: 0.8423 (tt0) cc_final: 0.8020 (pt0)
REVERT: C   73 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7530 (mp)
REVERT: C  183 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.7930 (m-30)
REVERT: C  187 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7470 (pt0)
REVERT: C  219 LEU cc_start: 0.7825 (mp) cc_final: 0.7555 (mp)
REVERT: C  222 GLU cc_start: 0.8420 (tt0) cc_final: 0.8027 (pt0)
REVERT: C  372 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7604 (mp)
REVERT: D   73 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7522 (mp)
REVERT: D  183 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.7978 (m-30)
REVERT: D  187 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7250 (mt-10)
REVERT: D  219 LEU cc_start: 0.7804 (mp) cc_final: 0.7539 (mp)
REVERT: D  222 GLU cc_start: 0.8392 (tt0) cc_final: 0.8008 (pt0)
  outliers start: 37
  outliers final: 24
  residues processed: 195
  average time/residue: 0.1146
  time to fit residues: 34.2506
Evaluate side-chains
  205 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 171
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  189 ASP
Chi-restraints excluded: chain A residue  247 GLN
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  516 PHE
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  183 ASP
Chi-restraints excluded: chain B residue  189 ASP
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  516 PHE
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  183 ASP
Chi-restraints excluded: chain C residue  189 ASP
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  516 PHE
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  183 ASP
Chi-restraints excluded: chain D residue  189 ASP
Chi-restraints excluded: chain D residue  291 LEU
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  516 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 171 optimal weight:    4.9990
   chunk 127 optimal weight:    1.9990
   chunk 157 optimal weight:    7.9990
   chunk 150 optimal weight:    1.9990
   chunk 182 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 44 optimal weight:    0.3980
   chunk 71 optimal weight:    2.9990
   chunk 180 optimal weight:    0.4980
   chunk 53 optimal weight:    4.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.155546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.106437 restraints weight = 20035.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 2.83
r_work: 0.3236 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  15536  Z= 0.142
  Angle     :  0.486   5.412  21020  Z= 0.269
  Chirality :  0.038   0.143   2376
  Planarity :  0.003   0.036   2604
  Dihedral  :  4.034  17.482   2016
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 12.95 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.24 (0.20), residues: 1844
  helix:  2.50 (0.15), residues: 1096
  sheet:  1.16 (0.34), residues: 220
  loop : -0.60 (0.28), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  57 
 TYR   0.016   0.001   TYR A 486 
 PHE   0.010   0.001   PHE D 225 
 TRP   0.007   0.001   TRP D 390 
 HIS   0.003   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (15532)
  covalent geometry    : angle       0.48628 (21012)
  SS BOND              : bond        0.00077 (    4)
  SS BOND              : angle       0.23708 (    8)
  hydrogen bonds       : bond        0.04110 (  993)
  hydrogen bonds       : angle       3.89057 ( 3135)

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

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

  3688 Ramachandran restraints generated.
    1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3688 Ramachandran restraints generated.
    1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 164
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7608 (mp)
REVERT: A  183 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7983 (m-30)
REVERT: A  187 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7107 (mt-10)
REVERT: A  200 LYS cc_start: 0.8178 (ttpt) cc_final: 0.7747 (tptp)
REVERT: A  222 GLU cc_start: 0.8395 (tt0) cc_final: 0.8035 (pt0)
REVERT: A  247 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7982 (tp40)
REVERT: A  372 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7588 (mp)
REVERT: B   73 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7619 (mp)
REVERT: B  183 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8032 (m-30)
REVERT: B  187 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7421 (pt0)
REVERT: B  222 GLU cc_start: 0.8406 (tt0) cc_final: 0.8039 (pt0)
REVERT: B  366 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6804 (tp30)
REVERT: B  372 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7639 (mp)
REVERT: C   73 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7613 (mp)
REVERT: C  183 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.7981 (m-30)
REVERT: C  187 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7450 (pt0)
REVERT: C  222 GLU cc_start: 0.8396 (tt0) cc_final: 0.8038 (pt0)
REVERT: C  366 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6810 (tp30)
REVERT: C  372 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7623 (mp)
REVERT: D   73 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7615 (mp)
REVERT: D  183 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8225 (m-30)
REVERT: D  219 LEU cc_start: 0.7884 (mp) cc_final: 0.7614 (mp)
REVERT: D  222 GLU cc_start: 0.8395 (tt0) cc_final: 0.8040 (pt0)
REVERT: D  247 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.8014 (tp40)
REVERT: D  366 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6811 (tp30)
REVERT: D  372 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7629 (mp)
  outliers start: 40
  outliers final: 23
  residues processed: 191
  average time/residue: 0.1167
  time to fit residues: 33.9894
Evaluate side-chains
  203 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 163
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  189 ASP
Chi-restraints excluded: chain A residue  247 GLN
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  516 PHE
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  183 ASP
Chi-restraints excluded: chain B residue  189 ASP
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  366 GLU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  516 PHE
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  183 ASP
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  366 GLU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  516 PHE
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  183 ASP
Chi-restraints excluded: chain D residue  189 ASP
Chi-restraints excluded: chain D residue  247 GLN
Chi-restraints excluded: chain D residue  291 LEU
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  366 GLU
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  516 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 111 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 131 optimal weight:    0.8980
   chunk 14 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 117 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 183 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 461 ASN
** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.154470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.104935 restraints weight = 19888.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 2.83
r_work: 0.3218 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  15536  Z= 0.164
  Angle     :  0.505   5.225  21020  Z= 0.279
  Chirality :  0.038   0.145   2376
  Planarity :  0.003   0.037   2604
  Dihedral  :  4.079  17.679   2016
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 13.25 %
    Favored  : 84.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.20 (0.20), residues: 1844
  helix:  2.45 (0.15), residues: 1096
  sheet:  1.28 (0.34), residues: 216
  loop : -0.64 (0.28), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 484 
 TYR   0.017   0.001   TYR C 486 
 PHE   0.009   0.001   PHE A 225 
 TRP   0.008   0.001   TRP D 390 
 HIS   0.004   0.001   HIS D 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (15532)
  covalent geometry    : angle       0.50519 (21012)
  SS BOND              : bond        0.00094 (    4)
  SS BOND              : angle       0.29515 (    8)
  hydrogen bonds       : bond        0.04320 (  993)
  hydrogen bonds       : angle       3.94377 ( 3135)

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

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

  3688 Ramachandran restraints generated.
    1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3688 Ramachandran restraints generated.
    1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 162
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7627 (mp)
REVERT: A  183 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8030 (m-30)
REVERT: A  200 LYS cc_start: 0.8168 (ttpt) cc_final: 0.7756 (tptp)
REVERT: A  222 GLU cc_start: 0.8417 (tt0) cc_final: 0.8065 (pt0)
REVERT: A  247 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7983 (tp40)
REVERT: A  366 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6822 (tp30)
REVERT: A  372 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7629 (mp)
REVERT: B   73 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7651 (mp)
REVERT: B  183 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8098 (m-30)
REVERT: B  187 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7414 (pt0)
REVERT: B  222 GLU cc_start: 0.8430 (tt0) cc_final: 0.8080 (pt0)
REVERT: B  366 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6826 (tp30)
REVERT: B  372 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7632 (mp)
REVERT: C   73 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7659 (mp)
REVERT: C  183 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8047 (m-30)
REVERT: C  187 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7366 (pt0)
REVERT: C  222 GLU cc_start: 0.8416 (tt0) cc_final: 0.8082 (pt0)
REVERT: C  366 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6871 (tp30)
REVERT: C  372 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7623 (mp)
REVERT: D   73 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7646 (mp)
REVERT: D  183 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8259 (m-30)
REVERT: D  222 GLU cc_start: 0.8410 (tt0) cc_final: 0.8080 (pt0)
REVERT: D  247 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.8018 (tp40)
REVERT: D  366 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6843 (tp30)
REVERT: D  372 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7641 (mp)
  outliers start: 42
  outliers final: 24
  residues processed: 191
  average time/residue: 0.1108
  time to fit residues: 32.1254
Evaluate side-chains
  199 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 157
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  189 ASP
Chi-restraints excluded: chain A residue  247 GLN
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  366 GLU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  516 PHE
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  183 ASP
Chi-restraints excluded: chain B residue  189 ASP
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  366 GLU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  516 PHE
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  183 ASP
Chi-restraints excluded: chain C residue  189 ASP
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  366 GLU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  516 PHE
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  183 ASP
Chi-restraints excluded: chain D residue  189 ASP
Chi-restraints excluded: chain D residue  247 GLN
Chi-restraints excluded: chain D residue  291 LEU
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  366 GLU
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  516 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 160 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 93 optimal weight:    0.2980
   chunk 30 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 178 optimal weight:    0.7980
   chunk 130 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.158506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.109289 restraints weight = 19880.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 2.88
r_work: 0.3277 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.3369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  15536  Z= 0.106
  Angle     :  0.447   5.009  21020  Z= 0.249
  Chirality :  0.036   0.130   2376
  Planarity :  0.003   0.037   2604
  Dihedral  :  3.809  17.128   2016
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.61 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.49 (0.20), residues: 1844
  helix:  2.67 (0.15), residues: 1096
  sheet:  1.29 (0.34), residues: 220
  loop : -0.44 (0.28), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  57 
 TYR   0.013   0.001   TYR A 486 
 PHE   0.011   0.001   PHE A 225 
 TRP   0.008   0.001   TRP A  64 
 HIS   0.003   0.001   HIS A 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 (15532)
  covalent geometry    : angle       0.44716 (21012)
  SS BOND              : bond        0.00043 (    4)
  SS BOND              : angle       0.04196 (    8)
  hydrogen bonds       : bond        0.03513 (  993)
  hydrogen bonds       : angle       3.71746 ( 3135)

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

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

  3688 Ramachandran restraints generated.
    1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3688 Ramachandran restraints generated.
    1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 176
  time to evaluate  : 0.600 
Fit side-chains
REVERT: A   73 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7547 (mp)
REVERT: A  169 LYS cc_start: 0.8435 (ttpt) cc_final: 0.7958 (mtpt)
REVERT: A  183 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.8017 (m-30)
REVERT: A  200 LYS cc_start: 0.8133 (ttpt) cc_final: 0.7708 (tptp)
REVERT: A  222 GLU cc_start: 0.8381 (tt0) cc_final: 0.8002 (pt0)
REVERT: A  247 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7994 (tp40)
REVERT: A  372 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7492 (mp)
REVERT: B   73 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7529 (mp)
REVERT: B  222 GLU cc_start: 0.8376 (tt0) cc_final: 0.8025 (pt0)
REVERT: B  247 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7866 (mm-40)
REVERT: B  372 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7545 (mp)
REVERT: C   73 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7532 (mp)
REVERT: C  183 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7982 (m-30)
REVERT: C  219 LEU cc_start: 0.7691 (mp) cc_final: 0.7421 (mp)
REVERT: C  222 GLU cc_start: 0.8374 (tt0) cc_final: 0.8014 (pt0)
REVERT: C  372 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7532 (mp)
REVERT: D   73 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7532 (mp)
REVERT: D  169 LYS cc_start: 0.8496 (ttpt) cc_final: 0.8034 (mtpt)
REVERT: D  219 LEU cc_start: 0.7707 (mp) cc_final: 0.7445 (mp)
REVERT: D  222 GLU cc_start: 0.8368 (tt0) cc_final: 0.8015 (pt0)
REVERT: D  247 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.8005 (tp40)
REVERT: D  372 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7556 (mp)
  outliers start: 33
  outliers final: 16
  residues processed: 199
  average time/residue: 0.1149
  time to fit residues: 35.3978
Evaluate side-chains
  194 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 165
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  247 GLN
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  516 PHE
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  189 ASP
Chi-restraints excluded: chain B residue  247 GLN
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  516 PHE
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  183 ASP
Chi-restraints excluded: chain C residue  189 ASP
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  516 PHE
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  189 ASP
Chi-restraints excluded: chain D residue  247 GLN
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  516 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 59 optimal weight:    0.0570
   chunk 118 optimal weight:    0.8980
   chunk 122 optimal weight:    0.9990
   chunk 113 optimal weight:    5.9990
   chunk 103 optimal weight:    6.9990
   chunk 119 optimal weight:   10.0000
   chunk 60 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    1.5904

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

Flipped N/Q/H residues before XYZ refinement:
** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.155994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.106374 restraints weight = 19796.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 2.85
r_work: 0.3236 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.3332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  15536  Z= 0.142
  Angle     :  0.490   7.458  21020  Z= 0.269
  Chirality :  0.038   0.135   2376
  Planarity :  0.003   0.036   2604
  Dihedral  :  3.896  17.347   2016
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.97 %
    Favored  : 84.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.44 (0.20), residues: 1844
  helix:  2.61 (0.15), residues: 1096
  sheet:  1.46 (0.34), residues: 216
  loop : -0.50 (0.28), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 484 
 TYR   0.016   0.001   TYR C 486 
 PHE   0.009   0.001   PHE D 225 
 TRP   0.007   0.001   TRP C 390 
 HIS   0.004   0.001   HIS C 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (15532)
  covalent geometry    : angle       0.48994 (21012)
  SS BOND              : bond        0.00076 (    4)
  SS BOND              : angle       0.33137 (    8)
  hydrogen bonds       : bond        0.04004 (  993)
  hydrogen bonds       : angle       3.80726 ( 3135)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3455.85 seconds
wall clock time: 60 minutes 9.83 seconds (3609.83 seconds total)