Starting phenix.real_space_refine
on Sun Aug 24 02:02:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f2k_50149/08_2025/9f2k_50149_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f2k_50149/08_2025/9f2k_50149.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f2k_50149/08_2025/9f2k_50149.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f2k_50149/08_2025/9f2k_50149.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f2k_50149/08_2025/9f2k_50149_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f2k_50149/08_2025/9f2k_50149_neut.cif"
  }
  resolution = 2.48
  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=  -0.001 sd=   0.035
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     S      72      5.16       5
     C   10220      2.51       5
     N    2788      2.21       5
     O    3096      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16184
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4002
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 513, 3986
          Classifications: {'peptide': 513}
          Link IDs: {'PTRANS': 24, 'TRANS': 488}
      Conformer: "B"
        Number of residues, atoms: 513, 3986
          Classifications: {'peptide': 513}
          Link IDs: {'PTRANS': 24, 'TRANS': 488}
          bond proxies already assigned to first conformer: 4049
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'NAD': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B, C, D
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N  AHIS A 167 " occ=0.75
      ... (18 atoms not shown)
      pdb=" NE2BHIS A 167 " occ=0.25
    residue:
      pdb=" N  AHIS B 167 " occ=0.75
      ... (18 atoms not shown)
      pdb=" NE2BHIS B 167 " occ=0.25
    residue:
      pdb=" N  AHIS C 167 " occ=0.75
      ... (18 atoms not shown)
      pdb=" NE2BHIS C 167 " occ=0.25
    residue:
      pdb=" N  AHIS D 167 " occ=0.75
      ... (18 atoms not shown)
      pdb=" NE2BHIS D 167 " occ=0.25
  Time building chain proxies: 3.65, per 1000 atoms: 0.23
  Number of scatterers: 16184
  At special positions: 0
  Unit cell: (105.61, 136.29, 99.71, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      72     16.00
     P       8     15.00
     O    3096      8.00
     N    2788      7.00
     C   10220      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3832

  Finding SS restraints...
    Secondary structure from input PDB file:
      80 helices and 20 sheets defined
      41.1% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 103 through 119
    Processing helix  chain 'A' and resid 136 through 141
    Processing helix  chain 'A' and resid 160 through 162
      No H-bonds generated for 'chain 'A' and resid 160 through 162'
    Processing helix  chain 'A' and resid 167 through 171
    Processing helix  chain 'A' and resid 182 through 191
    Processing helix  chain 'A' and resid 194 through 206
      removed outlier: 3.541A  pdb=" N   LEU A 200 " --> pdb=" O   SER A 196 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   LYS A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   GLU A 204 " --> pdb=" O   LEU A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 225
      removed outlier: 3.702A  pdb=" N   GLU A 225 " --> pdb=" O   ALA A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 257
      removed outlier: 3.969A  pdb=" N   VAL A 242 " --> pdb=" O   CYS A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 293
      removed outlier: 3.599A  pdb=" N   LYS A 291 " --> pdb=" O   LEU A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 311
    Processing helix  chain 'A' and resid 326 through 335
    Processing helix  chain 'A' and resid 346 through 360
      removed outlier: 3.509A  pdb=" N   ASP A 356 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 382
    Processing helix  chain 'A' and resid 384 through 397
      removed outlier: 4.377A  pdb=" N   SER A 390 " --> pdb=" O   ARG A 386 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LYS A 391 " --> pdb=" O   GLN A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 406
      removed outlier: 3.555A  pdb=" N   ASN A 406 " --> pdb=" O   MET A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 445
      No H-bonds generated for 'chain 'A' and resid 443 through 445'
    Processing helix  chain 'A' and resid 458 through 477
      Proline residue:  A 464  - end of helix
    Processing helix  chain 'A' and resid 489 through 493
      removed outlier: 3.533A  pdb=" N   TRP A 493 " --> pdb=" O   GLU A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 507
      removed outlier: 3.719A  pdb=" N   LEU A 503 " --> pdb=" O   LEU A 500 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   TYR A 505 " --> pdb=" O   ILE A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 536
    Processing helix  chain 'B' and resid 103 through 119
    Processing helix  chain 'B' and resid 136 through 141
    Processing helix  chain 'B' and resid 160 through 162
      No H-bonds generated for 'chain 'B' and resid 160 through 162'
    Processing helix  chain 'B' and resid 167 through 171
    Processing helix  chain 'B' and resid 182 through 191
    Processing helix  chain 'B' and resid 194 through 206
      removed outlier: 3.541A  pdb=" N   LEU B 200 " --> pdb=" O   SER B 196 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   LYS B 203 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   GLU B 204 " --> pdb=" O   LEU B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 225
      removed outlier: 3.702A  pdb=" N   GLU B 225 " --> pdb=" O   ALA B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 257
      removed outlier: 3.969A  pdb=" N   VAL B 242 " --> pdb=" O   CYS B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 293
      removed outlier: 3.599A  pdb=" N   LYS B 291 " --> pdb=" O   LEU B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 311
    Processing helix  chain 'B' and resid 326 through 335
    Processing helix  chain 'B' and resid 346 through 360
      removed outlier: 3.509A  pdb=" N   ASP B 356 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 382
    Processing helix  chain 'B' and resid 384 through 397
      removed outlier: 4.377A  pdb=" N   SER B 390 " --> pdb=" O   ARG B 386 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LYS B 391 " --> pdb=" O   GLN B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 406
      removed outlier: 3.555A  pdb=" N   ASN B 406 " --> pdb=" O   MET B 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 445
      No H-bonds generated for 'chain 'B' and resid 443 through 445'
    Processing helix  chain 'B' and resid 458 through 477
      Proline residue:  B 464  - end of helix
    Processing helix  chain 'B' and resid 489 through 493
      removed outlier: 3.533A  pdb=" N   TRP B 493 " --> pdb=" O   GLU B 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 507
      removed outlier: 3.719A  pdb=" N   LEU B 503 " --> pdb=" O   LEU B 500 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   TYR B 505 " --> pdb=" O   ILE B 502 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 521 through 536
    Processing helix  chain 'C' and resid 103 through 119
    Processing helix  chain 'C' and resid 136 through 141
    Processing helix  chain 'C' and resid 160 through 162
      No H-bonds generated for 'chain 'C' and resid 160 through 162'
    Processing helix  chain 'C' and resid 167 through 171
    Processing helix  chain 'C' and resid 182 through 191
    Processing helix  chain 'C' and resid 194 through 206
      removed outlier: 3.541A  pdb=" N   LEU C 200 " --> pdb=" O   SER C 196 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   LYS C 203 " --> pdb=" O   ALA C 199 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   GLU C 204 " --> pdb=" O   LEU C 200 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 221 through 225
      removed outlier: 3.702A  pdb=" N   GLU C 225 " --> pdb=" O   ALA C 222 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 257
      removed outlier: 3.969A  pdb=" N   VAL C 242 " --> pdb=" O   CYS C 238 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 282 through 293
      removed outlier: 3.599A  pdb=" N   LYS C 291 " --> pdb=" O   LEU C 287 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 311
    Processing helix  chain 'C' and resid 326 through 335
    Processing helix  chain 'C' and resid 346 through 360
      removed outlier: 3.509A  pdb=" N   ASP C 356 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 376 through 382
    Processing helix  chain 'C' and resid 384 through 397
      removed outlier: 4.377A  pdb=" N   SER C 390 " --> pdb=" O   ARG C 386 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LYS C 391 " --> pdb=" O   GLN C 387 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 399 through 406
      removed outlier: 3.555A  pdb=" N   ASN C 406 " --> pdb=" O   MET C 402 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 443 through 445
      No H-bonds generated for 'chain 'C' and resid 443 through 445'
    Processing helix  chain 'C' and resid 458 through 477
      Proline residue:  C 464  - end of helix
    Processing helix  chain 'C' and resid 489 through 493
      removed outlier: 3.533A  pdb=" N   TRP C 493 " --> pdb=" O   GLU C 490 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 500 through 507
      removed outlier: 3.719A  pdb=" N   LEU C 503 " --> pdb=" O   LEU C 500 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   TYR C 505 " --> pdb=" O   ILE C 502 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 521 through 536
    Processing helix  chain 'D' and resid 103 through 119
    Processing helix  chain 'D' and resid 136 through 141
    Processing helix  chain 'D' and resid 160 through 162
      No H-bonds generated for 'chain 'D' and resid 160 through 162'
    Processing helix  chain 'D' and resid 167 through 171
    Processing helix  chain 'D' and resid 182 through 191
    Processing helix  chain 'D' and resid 194 through 206
      removed outlier: 3.541A  pdb=" N   LEU D 200 " --> pdb=" O   SER D 196 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   LYS D 203 " --> pdb=" O   ALA D 199 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   GLU D 204 " --> pdb=" O   LEU D 200 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 221 through 225
      removed outlier: 3.702A  pdb=" N   GLU D 225 " --> pdb=" O   ALA D 222 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 238 through 257
      removed outlier: 3.969A  pdb=" N   VAL D 242 " --> pdb=" O   CYS D 238 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 282 through 293
      removed outlier: 3.599A  pdb=" N   LYS D 291 " --> pdb=" O   LEU D 287 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 311
    Processing helix  chain 'D' and resid 326 through 335
    Processing helix  chain 'D' and resid 346 through 360
      removed outlier: 3.509A  pdb=" N   ASP D 356 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 376 through 382
    Processing helix  chain 'D' and resid 384 through 397
      removed outlier: 4.377A  pdb=" N   SER D 390 " --> pdb=" O   ARG D 386 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LYS D 391 " --> pdb=" O   GLN D 387 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 399 through 406
      removed outlier: 3.555A  pdb=" N   ASN D 406 " --> pdb=" O   MET D 402 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 443 through 445
      No H-bonds generated for 'chain 'D' and resid 443 through 445'
    Processing helix  chain 'D' and resid 458 through 477
      Proline residue:  D 464  - end of helix
    Processing helix  chain 'D' and resid 489 through 493
      removed outlier: 3.533A  pdb=" N   TRP D 493 " --> pdb=" O   GLU D 490 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 500 through 507
      removed outlier: 3.719A  pdb=" N   LEU D 503 " --> pdb=" O   LEU D 500 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   TYR D 505 " --> pdb=" O   ILE D 502 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 521 through 536
    Processing sheet with id=1, first strand: chain 'A' and resid 57 through 68
    Processing sheet with id=2, first strand: chain 'A' and resid 172 through 176
    Processing sheet with id=3, first strand: chain 'A' and resid 121 through 124
    Processing sheet with id=4, first strand: chain 'A' and resid 142 through 147
      removed outlier: 5.237A  pdb=" N   LYS A 144 " --> pdb=" O   ILE A 157 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ILE A 157 " --> pdb=" O   LYS A 144 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLY A 146 " --> pdb=" O   ILE A 155 " (cutoff:3.500A)
    Processing sheet with id=5, first strand: chain 'A' and resid 417 through 424
      removed outlier: 5.585A  pdb=" N   LEU A 365 " --> pdb=" O   GLU A 441 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   GLU A 441 " --> pdb=" O   LEU A 365 " (cutoff:3.500A)
    Processing sheet with id=6, first strand: chain 'B' and resid 57 through 68
    Processing sheet with id=7, first strand: chain 'B' and resid 172 through 176
    Processing sheet with id=8, first strand: chain 'B' and resid 121 through 124
    Processing sheet with id=9, first strand: chain 'B' and resid 142 through 147
      removed outlier: 5.237A  pdb=" N   LYS B 144 " --> pdb=" O   ILE B 157 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ILE B 157 " --> pdb=" O   LYS B 144 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLY B 146 " --> pdb=" O   ILE B 155 " (cutoff:3.500A)
    Processing sheet with id=10, first strand: chain 'B' and resid 417 through 424
      removed outlier: 5.585A  pdb=" N   LEU B 365 " --> pdb=" O   GLU B 441 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   GLU B 441 " --> pdb=" O   LEU B 365 " (cutoff:3.500A)
    Processing sheet with id=11, first strand: chain 'C' and resid 57 through 68
    Processing sheet with id=12, first strand: chain 'C' and resid 172 through 176
    Processing sheet with id=13, first strand: chain 'C' and resid 121 through 124
    Processing sheet with id=14, first strand: chain 'C' and resid 142 through 147
      removed outlier: 5.237A  pdb=" N   LYS C 144 " --> pdb=" O   ILE C 157 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ILE C 157 " --> pdb=" O   LYS C 144 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLY C 146 " --> pdb=" O   ILE C 155 " (cutoff:3.500A)
    Processing sheet with id=15, first strand: chain 'C' and resid 417 through 424
      removed outlier: 5.585A  pdb=" N   LEU C 365 " --> pdb=" O   GLU C 441 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   GLU C 441 " --> pdb=" O   LEU C 365 " (cutoff:3.500A)
    Processing sheet with id=16, first strand: chain 'D' and resid 57 through 68
    Processing sheet with id=17, first strand: chain 'D' and resid 172 through 176
    Processing sheet with id=18, first strand: chain 'D' and resid 121 through 124
    Processing sheet with id=19, first strand: chain 'D' and resid 142 through 147
      removed outlier: 5.237A  pdb=" N   LYS D 144 " --> pdb=" O   ILE D 157 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ILE D 157 " --> pdb=" O   LYS D 144 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLY D 146 " --> pdb=" O   ILE D 155 " (cutoff:3.500A)
    Processing sheet with id=20, first strand: chain 'D' and resid 417 through 424
      removed outlier: 5.585A  pdb=" N   LEU D 365 " --> pdb=" O   GLU D 441 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   GLU D 441 " --> pdb=" O   LEU D 365 " (cutoff:3.500A)

    740 hydrogen bonds defined for protein.
    2052 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: 2.88

  Time building geometry restraints manager: 1.35 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 5368
        1.34 -     1.46: 3376
        1.46 -     1.58: 7652
        1.58 -     1.69: 16
        1.69 -     1.81: 128
  Bond restraints: 16540
  Sorted by residual:
  bond pdb=" N   ILE D 109 "
       pdb=" CA  ILE D 109 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.032 1.17e-02 7.31e+03 7.65e+00
  bond pdb=" N   ILE A 109 "
       pdb=" CA  ILE A 109 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.032 1.17e-02 7.31e+03 7.65e+00
  bond pdb=" N   ILE C 109 "
       pdb=" CA  ILE C 109 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.032 1.17e-02 7.31e+03 7.65e+00
  bond pdb=" N   ILE B 109 "
       pdb=" CA  ILE B 109 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.032 1.17e-02 7.31e+03 7.65e+00
  bond pdb=" O3  NAD D 601 "
       pdb=" PA  NAD D 601 "
    ideal  model  delta    sigma   weight residual
    1.653  1.600  0.053 2.00e-02 2.50e+03 7.05e+00
  ... (remaining 16535 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 22004
        1.91 -     3.82: 404
        3.82 -     5.74: 68
        5.74 -     7.65: 12
        7.65 -     9.56: 4
  Bond angle restraints: 22492
  Sorted by residual:
  angle pdb=" PA  NAD A 601 "
        pdb=" O3  NAD A 601 "
        pdb=" PN  NAD A 601 "
      ideal   model   delta    sigma   weight residual
     126.50  136.06   -9.56 3.00e+00 1.11e-01 1.02e+01
  angle pdb=" PA  NAD C 601 "
        pdb=" O3  NAD C 601 "
        pdb=" PN  NAD C 601 "
      ideal   model   delta    sigma   weight residual
     126.50  136.06   -9.56 3.00e+00 1.11e-01 1.02e+01
  angle pdb=" PA  NAD D 601 "
        pdb=" O3  NAD D 601 "
        pdb=" PN  NAD D 601 "
      ideal   model   delta    sigma   weight residual
     126.50  136.06   -9.56 3.00e+00 1.11e-01 1.02e+01
  angle pdb=" PA  NAD B 601 "
        pdb=" O3  NAD B 601 "
        pdb=" PN  NAD B 601 "
      ideal   model   delta    sigma   weight residual
     126.50  136.06   -9.56 3.00e+00 1.11e-01 1.02e+01
  angle pdb=" CA  ILE D 109 "
        pdb=" C   ILE D 109 "
        pdb=" O   ILE D 109 "
      ideal   model   delta    sigma   weight residual
     121.17  118.15    3.02 1.06e+00 8.90e-01 8.14e+00
  ... (remaining 22487 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 8744
       17.56 -    35.13: 988
       35.13 -    52.69: 296
       52.69 -    70.26: 48
       70.26 -    87.82: 20
  Dihedral angle restraints: 10096
    sinusoidal: 4140
      harmonic: 5956
  Sorted by residual:
  dihedral pdb=" CB  GLU A 225 "
           pdb=" CG  GLU A 225 "
           pdb=" CD  GLU A 225 "
           pdb=" OE1 GLU A 225 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.82   87.82     1      3.00e+01 1.11e-03 1.03e+01
  dihedral pdb=" CB  GLU D 225 "
           pdb=" CG  GLU D 225 "
           pdb=" CD  GLU D 225 "
           pdb=" OE1 GLU D 225 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.82   87.82     1      3.00e+01 1.11e-03 1.03e+01
  dihedral pdb=" CB  GLU C 225 "
           pdb=" CG  GLU C 225 "
           pdb=" CD  GLU C 225 "
           pdb=" OE1 GLU C 225 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.82   87.82     1      3.00e+01 1.11e-03 1.03e+01
  ... (remaining 10093 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1968
       0.045 -    0.090: 368
       0.090 -    0.135: 204
       0.135 -    0.179: 0
       0.179 -    0.224: 4
  Chirality restraints: 2544
  Sorted by residual:
  chirality pdb=" CA  ILE D 109 "
            pdb=" N   ILE D 109 "
            pdb=" C   ILE D 109 "
            pdb=" CB  ILE D 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  ILE A 109 "
            pdb=" N   ILE A 109 "
            pdb=" C   ILE A 109 "
            pdb=" CB  ILE A 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  ILE B 109 "
            pdb=" N   ILE B 109 "
            pdb=" C   ILE B 109 "
            pdb=" CB  ILE B 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.26e+00
  ... (remaining 2541 not shown)

  Planarity restraints: 2896
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR D 110 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.70e+00
        pdb=" C   THR D 110 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   THR D 110 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ALA D 111 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C 110 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.70e+00
        pdb=" C   THR C 110 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   THR C 110 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ALA C 111 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 110 "   -0.011 2.00e-02 2.50e+03   2.17e-02 4.70e+00
        pdb=" C   THR B 110 "    0.038 2.00e-02 2.50e+03
        pdb=" O   THR B 110 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ALA B 111 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 2893 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 144
        2.60 -     3.18: 13076
        3.18 -     3.75: 25460
        3.75 -     4.33: 38548
        4.33 -     4.90: 62840
  Nonbonded interactions: 140068
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN D 347 "
            pdb=" OD1 ASP D 436 "
     model   vdw
     2.026 3.040
  nonbonded pdb=" OE1 GLN B 347 "
            pdb=" OD1 ASP B 436 "
     model   vdw
     2.026 3.040
  nonbonded pdb=" OE1 GLN C 347 "
            pdb=" OD1 ASP C 436 "
     model   vdw
     2.026 3.040
  nonbonded pdb=" OE1 GLN A 347 "
            pdb=" OD1 ASP A 436 "
     model   vdw
     2.026 3.040
  nonbonded pdb=" OG  SER C 136 "
            pdb=" OD1 ASP C 468 "
     model   vdw
     2.131 3.040
  ... (remaining 140063 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  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=0.25 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:             11.010
  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:          0.280
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.480
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
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      :  0.004   0.053  16540  Z= 0.200
  Angle     :  0.638   9.559  22492  Z= 0.327
  Chirality :  0.044   0.224   2544
  Planarity :  0.005   0.041   2896
  Dihedral  : 16.420  87.819   6264
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 21.00 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.18), residues: 2060
  helix: -0.22 (0.18), residues: 748
  sheet:  0.88 (0.27), residues: 376
  loop : -0.15 (0.19), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 333 
 TYR   0.006   0.001   TYR A  50 
 PHE   0.008   0.001   PHE D 219 
 TRP   0.011   0.001   TRP A 122 
 HIS   0.003   0.001   HIS C 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 (16540)
  covalent geometry    : angle       0.63810 (22492)
  hydrogen bonds       : bond        0.16328 (  740)
  hydrogen bonds       : angle       5.98026 ( 2052)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 192
  time to evaluate  : 0.576 
Fit side-chains
  outliers start: 20
  outliers final: 20
  residues processed: 208
  average time/residue: 0.5422
  time to fit residues: 124.5566
Evaluate side-chains
  208 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 188
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  260 LYS
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  436 ASP
Chi-restraints excluded: chain A residue  456 CYS
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  260 LYS
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  436 ASP
Chi-restraints excluded: chain B residue  456 CYS
Chi-restraints excluded: chain C residue  196 SER
Chi-restraints excluded: chain C residue  260 LYS
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  436 ASP
Chi-restraints excluded: chain C residue  456 CYS
Chi-restraints excluded: chain D residue  196 SER
Chi-restraints excluded: chain D residue  260 LYS
Chi-restraints excluded: chain D residue  398 VAL
Chi-restraints excluded: chain D residue  436 ASP
Chi-restraints excluded: chain D residue  456 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 194 optimal weight:    0.9980
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    4.9990
   chunk 200 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    5.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 288 ASN
A 316 ASN
A 347 GLN
A 372 ASN
B 288 ASN
B 316 ASN
B 347 GLN
B 372 ASN
C 288 ASN
C 316 ASN
C 347 GLN
C 372 ASN
D 288 ASN
D 316 ASN
D 347 GLN
D 372 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.159324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.140548 restraints weight = 55149.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 2.33
r_work: 0.3502 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3391 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3386
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3386 r_free = 0.3386    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3386 r_free = 0.3386    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3386
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.069  16540  Z= 0.293
  Angle     :  0.755   8.549  22492  Z= 0.402
  Chirality :  0.051   0.227   2544
  Planarity :  0.006   0.041   2896
  Dihedral  :  9.308  59.541   2464
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 16.89 %
    Favored  : 79.68 %
  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:  0.22 (0.18), residues: 2060
  helix:  0.01 (0.18), residues: 732
  sheet:  1.06 (0.26), residues: 392
  loop :  0.02 (0.20), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 125 
 TYR   0.013   0.002   TYR B 134 
 PHE   0.017   0.003   PHE D 552 
 TRP   0.012   0.002   TRP D 101 
 HIS   0.009   0.002   HIS C 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00671 (16540)
  covalent geometry    : angle       0.75452 (22492)
  hydrogen bonds       : bond        0.06487 (  740)
  hydrogen bonds       : angle       5.20576 ( 2052)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 196
  time to evaluate  : 0.548 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7899 (mpt180)
REVERT: A  125 ARG cc_start: 0.7399 (ptm-80) cc_final: 0.7163 (ptm-80)
REVERT: A  209 LYS cc_start: 0.7706 (tptm) cc_final: 0.7457 (tptm)
REVERT: A  223 ASN cc_start: 0.7969 (p0) cc_final: 0.7613 (p0)
REVERT: A  332 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7750 (mt-10)
REVERT: A  432 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.7975 (tmmm)
REVERT: A  490 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7170 (mp0)
REVERT: B   79 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7897 (mpt180)
REVERT: B  125 ARG cc_start: 0.7410 (ptm-80) cc_final: 0.7176 (ptm-80)
REVERT: B  209 LYS cc_start: 0.7706 (tptm) cc_final: 0.7459 (tptm)
REVERT: B  223 ASN cc_start: 0.7984 (p0) cc_final: 0.7621 (p0)
REVERT: B  332 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7751 (mt-10)
REVERT: B  432 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.7977 (tmmm)
REVERT: B  490 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7161 (mp0)
REVERT: C   79 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7895 (mpt180)
REVERT: C  125 ARG cc_start: 0.7408 (ptm-80) cc_final: 0.7174 (ptm-80)
REVERT: C  209 LYS cc_start: 0.7708 (tptm) cc_final: 0.7460 (tptm)
REVERT: C  223 ASN cc_start: 0.7973 (p0) cc_final: 0.7604 (p0)
REVERT: C  332 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7753 (mt-10)
REVERT: C  432 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.7966 (tmmm)
REVERT: C  490 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7173 (mp0)
REVERT: D   79 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7882 (mpt180)
REVERT: D  125 ARG cc_start: 0.7412 (ptm-80) cc_final: 0.7174 (ptm-80)
REVERT: D  209 LYS cc_start: 0.7711 (tptm) cc_final: 0.7464 (tptm)
REVERT: D  223 ASN cc_start: 0.7998 (p0) cc_final: 0.7608 (p0)
REVERT: D  332 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7754 (mt-10)
REVERT: D  432 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.7961 (tmmm)
REVERT: D  490 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7154 (mp0)
  outliers start: 60
  outliers final: 24
  residues processed: 248
  average time/residue: 0.5648
  time to fit residues: 154.1367
Evaluate side-chains
  208 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 172
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  357 PHE
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain A residue  456 CYS
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  432 LYS
Chi-restraints excluded: chain B residue  456 CYS
Chi-restraints excluded: chain B residue  489 THR
Chi-restraints excluded: chain B residue  490 GLU
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  357 PHE
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  432 LYS
Chi-restraints excluded: chain C residue  456 CYS
Chi-restraints excluded: chain C residue  489 THR
Chi-restraints excluded: chain C residue  490 GLU
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  357 PHE
Chi-restraints excluded: chain D residue  370 SER
Chi-restraints excluded: chain D residue  398 VAL
Chi-restraints excluded: chain D residue  432 LYS
Chi-restraints excluded: chain D residue  456 CYS
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  490 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 160 optimal weight:    0.8980
   chunk 137 optimal weight:    0.9990
   chunk 166 optimal weight:    0.1980
   chunk 83 optimal weight:    0.4980
   chunk 64 optimal weight:    4.9990
   chunk 144 optimal weight:    2.9990
   chunk 152 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 117 optimal weight:    3.9990
   chunk 193 optimal weight:    0.9990
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 288 ASN
A 387 GLN
B 288 ASN
B 387 GLN
C 288 ASN
C 387 GLN
D 288 ASN
D 387 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.165663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.146774 restraints weight = 57047.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 2.34
r_work: 0.3565 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3562
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3562
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.1897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  16540  Z= 0.127
  Angle     :  0.541   6.456  22492  Z= 0.287
  Chirality :  0.043   0.129   2544
  Planarity :  0.004   0.037   2896
  Dihedral  :  8.307  61.746   2436
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 15.98 %
    Favored  : 81.05 %
  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:  0.57 (0.18), residues: 2060
  helix:  0.48 (0.18), residues: 760
  sheet:  1.36 (0.26), residues: 376
  loop :  0.00 (0.20), residues: 924

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 227 
 TYR   0.005   0.001   TYR D 134 
 PHE   0.008   0.001   PHE B 552 
 TRP   0.010   0.001   TRP D 176 
 HIS   0.006   0.001   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (16540)
  covalent geometry    : angle       0.54140 (22492)
  hydrogen bonds       : bond        0.04171 (  740)
  hydrogen bonds       : angle       4.81693 ( 2052)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 212
  time to evaluate  : 0.648 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7814 (mpt180)
REVERT: A  218 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7191 (p0)
REVERT: A  350 MET cc_start: 0.8696 (ttm) cc_final: 0.8393 (ttp)
REVERT: A  354 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7961 (tp)
REVERT: A  490 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7240 (mp0)
REVERT: B   79 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7798 (mpt180)
REVERT: B  218 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7177 (p0)
REVERT: B  350 MET cc_start: 0.8699 (ttm) cc_final: 0.8395 (ttp)
REVERT: B  354 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7956 (tp)
REVERT: B  490 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7231 (mp0)
REVERT: C   79 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7815 (mpt180)
REVERT: C  218 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7192 (p0)
REVERT: C  350 MET cc_start: 0.8695 (ttm) cc_final: 0.8398 (ttp)
REVERT: C  354 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7958 (tp)
REVERT: C  490 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7242 (mp0)
REVERT: D   79 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7797 (mpt180)
REVERT: D  218 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.7185 (p0)
REVERT: D  350 MET cc_start: 0.8696 (ttm) cc_final: 0.8391 (ttp)
REVERT: D  354 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7954 (tp)
REVERT: D  490 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7238 (mp0)
  outliers start: 52
  outliers final: 16
  residues processed: 252
  average time/residue: 0.6241
  time to fit residues: 172.1666
Evaluate side-chains
  224 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 192
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  456 CYS
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue  218 ASP
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  456 CYS
Chi-restraints excluded: chain B residue  490 GLU
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  218 ASP
Chi-restraints excluded: chain C residue  264 LEU
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  456 CYS
Chi-restraints excluded: chain C residue  490 GLU
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  218 ASP
Chi-restraints excluded: chain D residue  264 LEU
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  370 SER
Chi-restraints excluded: chain D residue  398 VAL
Chi-restraints excluded: chain D residue  456 CYS
Chi-restraints excluded: chain D residue  490 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 109 optimal weight:    1.9990
   chunk 191 optimal weight:    0.6980
   chunk 26 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 146 optimal weight:    6.9990
   chunk 159 optimal weight:    4.9990
   chunk 185 optimal weight:    6.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 223 ASN
B 223 ASN
C 223 ASN
D 223 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.161117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.142109 restraints weight = 61418.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.45
r_work: 0.3507 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3503
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3503 r_free = 0.3503    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3503 r_free = 0.3503    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3503
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  16540  Z= 0.207
  Angle     :  0.637   8.153  22492  Z= 0.338
  Chirality :  0.046   0.148   2544
  Planarity :  0.005   0.038   2896
  Dihedral  :  8.795  59.996   2436
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 14.61 %
    Favored  : 81.28 %
  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:  0.44 (0.18), residues: 2060
  helix:  0.30 (0.18), residues: 764
  sheet:  1.05 (0.26), residues: 364
  loop :  0.14 (0.20), residues: 932

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 227 
 TYR   0.008   0.001   TYR A 505 
 PHE   0.012   0.002   PHE D 552 
 TRP   0.010   0.002   TRP D 176 
 HIS   0.006   0.001   HIS B 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 (16540)
  covalent geometry    : angle       0.63699 (22492)
  hydrogen bonds       : bond        0.05380 (  740)
  hydrogen bonds       : angle       4.99127 ( 2052)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 184
  time to evaluate  : 0.627 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7783 (mpt180)
REVERT: A  125 ARG cc_start: 0.7373 (ptm-80) cc_final: 0.7167 (ptm-80)
REVERT: A  194 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6997 (mm-30)
REVERT: A  218 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7257 (p0)
REVERT: A  240 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6397 (mm-30)
REVERT: A  350 MET cc_start: 0.8786 (ttm) cc_final: 0.8490 (ttp)
REVERT: A  437 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7609 (tm-30)
REVERT: A  490 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7198 (mp0)
REVERT: B   79 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7787 (mpt180)
REVERT: B  125 ARG cc_start: 0.7376 (ptm-80) cc_final: 0.7168 (ptm-80)
REVERT: B  194 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.7005 (mm-30)
REVERT: B  218 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7253 (p0)
REVERT: B  240 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6412 (mm-30)
REVERT: B  350 MET cc_start: 0.8793 (ttm) cc_final: 0.8497 (ttp)
REVERT: B  437 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7605 (tm-30)
REVERT: B  490 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7199 (mp0)
REVERT: C   79 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7785 (mpt180)
REVERT: C  125 ARG cc_start: 0.7376 (ptm-80) cc_final: 0.7172 (ptm-80)
REVERT: C  194 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.7003 (mm-30)
REVERT: C  218 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7253 (p0)
REVERT: C  240 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6387 (mm-30)
REVERT: C  350 MET cc_start: 0.8789 (ttm) cc_final: 0.8492 (ttp)
REVERT: C  437 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7606 (tm-30)
REVERT: C  490 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7207 (mp0)
REVERT: D   79 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7786 (mpt180)
REVERT: D  125 ARG cc_start: 0.7376 (ptm-80) cc_final: 0.7169 (ptm-80)
REVERT: D  194 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.7002 (mm-30)
REVERT: D  218 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7255 (p0)
REVERT: D  240 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6393 (mm-30)
REVERT: D  350 MET cc_start: 0.8792 (ttm) cc_final: 0.8495 (ttp)
REVERT: D  437 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7604 (tm-30)
REVERT: D  490 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7205 (mp0)
  outliers start: 72
  outliers final: 36
  residues processed: 236
  average time/residue: 0.5859
  time to fit residues: 153.1669
Evaluate side-chains
  248 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 188
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain A residue  456 CYS
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue  187 MET
Chi-restraints excluded: chain B residue  194 GLU
Chi-restraints excluded: chain B residue  218 ASP
Chi-restraints excluded: chain B residue  238 CYS
Chi-restraints excluded: chain B residue  240 GLU
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  437 GLU
Chi-restraints excluded: chain B residue  456 CYS
Chi-restraints excluded: chain B residue  489 THR
Chi-restraints excluded: chain B residue  490 GLU
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  187 MET
Chi-restraints excluded: chain C residue  194 GLU
Chi-restraints excluded: chain C residue  218 ASP
Chi-restraints excluded: chain C residue  238 CYS
Chi-restraints excluded: chain C residue  240 GLU
Chi-restraints excluded: chain C residue  264 LEU
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  437 GLU
Chi-restraints excluded: chain C residue  456 CYS
Chi-restraints excluded: chain C residue  489 THR
Chi-restraints excluded: chain C residue  490 GLU
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  187 MET
Chi-restraints excluded: chain D residue  194 GLU
Chi-restraints excluded: chain D residue  218 ASP
Chi-restraints excluded: chain D residue  238 CYS
Chi-restraints excluded: chain D residue  240 GLU
Chi-restraints excluded: chain D residue  264 LEU
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  370 SER
Chi-restraints excluded: chain D residue  398 VAL
Chi-restraints excluded: chain D residue  437 GLU
Chi-restraints excluded: chain D residue  456 CYS
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  490 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 147 optimal weight:    7.9990
   chunk 98 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   chunk 139 optimal weight:    0.6980
   chunk 106 optimal weight:    4.9990
   chunk 180 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 117 optimal weight:    0.9990
   chunk 160 optimal weight:    0.6980
   chunk 4 optimal weight:    4.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 387 GLN
B 387 GLN
C 387 GLN
D 387 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.165739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.147422 restraints weight = 49060.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3700 rms_B_bonded: 2.16
r_work: 0.3586 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3479 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3473
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3473 r_free = 0.3473    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3473 r_free = 0.3473    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3473
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  16540  Z= 0.125
  Angle     :  0.532   6.291  22492  Z= 0.282
  Chirality :  0.043   0.123   2544
  Planarity :  0.004   0.035   2896
  Dihedral  :  8.265  61.718   2436
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.50 %
    Favored  : 81.05 %
  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:  0.79 (0.18), residues: 2060
  helix:  0.69 (0.18), residues: 756
  sheet:  1.42 (0.26), residues: 348
  loop :  0.17 (0.20), residues: 956

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 125 
 TYR   0.004   0.001   TYR A 505 
 PHE   0.007   0.001   PHE C 552 
 TRP   0.011   0.001   TRP D 176 
 HIS   0.006   0.001   HIS B 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (16540)
  covalent geometry    : angle       0.53187 (22492)
  hydrogen bonds       : bond        0.04089 (  740)
  hydrogen bonds       : angle       4.74202 ( 2052)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 196
  time to evaluate  : 0.602 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7918 (mpt180)
REVERT: A  218 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7207 (p0)
REVERT: A  350 MET cc_start: 0.8820 (ttm) cc_final: 0.8512 (ttp)
REVERT: A  354 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8009 (tt)
REVERT: A  437 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7627 (tm-30)
REVERT: A  490 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7306 (mp0)
REVERT: B   79 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7935 (mpt180)
REVERT: B  218 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7210 (p0)
REVERT: B  350 MET cc_start: 0.8821 (ttm) cc_final: 0.8514 (ttp)
REVERT: B  354 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.8012 (tt)
REVERT: B  437 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7619 (tm-30)
REVERT: B  490 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7306 (mp0)
REVERT: C   79 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7945 (mpt180)
REVERT: C  218 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7214 (p0)
REVERT: C  350 MET cc_start: 0.8821 (ttm) cc_final: 0.8516 (ttp)
REVERT: C  354 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8016 (tt)
REVERT: C  437 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7637 (tm-30)
REVERT: C  490 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7298 (mp0)
REVERT: D   79 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7924 (mpt180)
REVERT: D  194 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7172 (mm-30)
REVERT: D  218 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7209 (p0)
REVERT: D  350 MET cc_start: 0.8821 (ttm) cc_final: 0.8514 (ttp)
REVERT: D  354 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8019 (tt)
REVERT: D  437 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7618 (tm-30)
REVERT: D  490 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7302 (mp0)
  outliers start: 43
  outliers final: 15
  residues processed: 223
  average time/residue: 0.6179
  time to fit residues: 150.4838
Evaluate side-chains
  220 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 184
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue  218 ASP
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  437 GLU
Chi-restraints excluded: chain B residue  490 GLU
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  218 ASP
Chi-restraints excluded: chain C residue  264 LEU
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  437 GLU
Chi-restraints excluded: chain C residue  490 GLU
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  194 GLU
Chi-restraints excluded: chain D residue  218 ASP
Chi-restraints excluded: chain D residue  264 LEU
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  370 SER
Chi-restraints excluded: chain D residue  398 VAL
Chi-restraints excluded: chain D residue  437 GLU
Chi-restraints excluded: chain D residue  490 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 183 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 90 optimal weight:    7.9990
   chunk 72 optimal weight:    6.9990
   chunk 100 optimal weight:    5.9990
   chunk 101 optimal weight:    0.5980
   chunk 71 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.5184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.162420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.143928 restraints weight = 46667.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 2.09
r_work: 0.3556 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3450 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3444
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3444 r_free = 0.3444    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3444 r_free = 0.3444    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3444
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  16540  Z= 0.177
  Angle     :  0.597   8.282  22492  Z= 0.315
  Chirality :  0.044   0.131   2544
  Planarity :  0.004   0.036   2896
  Dihedral  :  8.529  60.358   2432
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 15.70 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.18), residues: 2060
  helix:  0.38 (0.18), residues: 780
  sheet:  1.06 (0.26), residues: 352
  loop :  0.31 (0.20), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 125 
 TYR   0.007   0.001   TYR B 505 
 PHE   0.010   0.001   PHE D 552 
 TRP   0.011   0.002   TRP D 176 
 HIS   0.006   0.001   HIS B 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (16540)
  covalent geometry    : angle       0.59652 (22492)
  hydrogen bonds       : bond        0.04920 (  740)
  hydrogen bonds       : angle       4.86308 ( 2052)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 176
  time to evaluate  : 0.479 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7826 (mpt180)
REVERT: A  218 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7254 (p0)
REVERT: A  240 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6440 (mm-30)
REVERT: A  350 MET cc_start: 0.8857 (ttm) cc_final: 0.8566 (ttp)
REVERT: A  354 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8076 (tt)
REVERT: A  437 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7650 (tm-30)
REVERT: A  490 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7252 (mp0)
REVERT: B   79 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7844 (mpt180)
REVERT: B  218 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7255 (p0)
REVERT: B  240 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6453 (mm-30)
REVERT: B  350 MET cc_start: 0.8864 (ttm) cc_final: 0.8576 (ttp)
REVERT: B  354 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8077 (tt)
REVERT: B  437 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7669 (tm-30)
REVERT: B  490 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7252 (mp0)
REVERT: C   79 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7810 (mpt180)
REVERT: C  218 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7248 (p0)
REVERT: C  240 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6470 (mm-30)
REVERT: C  350 MET cc_start: 0.8849 (ttm) cc_final: 0.8560 (ttp)
REVERT: C  354 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8087 (tt)
REVERT: C  437 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7673 (tm-30)
REVERT: C  490 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7256 (mp0)
REVERT: D   79 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7871 (mpt180)
REVERT: D  194 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7126 (mm-30)
REVERT: D  218 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7247 (p0)
REVERT: D  240 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6467 (mm-30)
REVERT: D  350 MET cc_start: 0.8860 (ttm) cc_final: 0.8571 (ttp)
REVERT: D  354 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8077 (tt)
REVERT: D  437 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7668 (tm-30)
REVERT: D  490 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7269 (mp0)
  outliers start: 61
  outliers final: 24
  residues processed: 217
  average time/residue: 0.5781
  time to fit residues: 138.1853
Evaluate side-chains
  213 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 164
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue  218 ASP
Chi-restraints excluded: chain B residue  238 CYS
Chi-restraints excluded: chain B residue  240 GLU
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  437 GLU
Chi-restraints excluded: chain B residue  489 THR
Chi-restraints excluded: chain B residue  490 GLU
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  218 ASP
Chi-restraints excluded: chain C residue  238 CYS
Chi-restraints excluded: chain C residue  240 GLU
Chi-restraints excluded: chain C residue  264 LEU
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  437 GLU
Chi-restraints excluded: chain C residue  489 THR
Chi-restraints excluded: chain C residue  490 GLU
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  194 GLU
Chi-restraints excluded: chain D residue  218 ASP
Chi-restraints excluded: chain D residue  238 CYS
Chi-restraints excluded: chain D residue  240 GLU
Chi-restraints excluded: chain D residue  264 LEU
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  370 SER
Chi-restraints excluded: chain D residue  398 VAL
Chi-restraints excluded: chain D residue  437 GLU
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  490 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 150 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 110 optimal weight:    0.0870
   chunk 25 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 125 optimal weight:    5.9990
   chunk 164 optimal weight:    2.9990
   chunk 61 optimal weight:    8.9990
   chunk 153 optimal weight:    0.4980
   chunk 155 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.6962

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.166193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.147423 restraints weight = 53410.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 2.29
r_work: 0.3584 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3475 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3469
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3469
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  16540  Z= 0.121
  Angle     :  0.524   6.909  22492  Z= 0.277
  Chirality :  0.042   0.123   2544
  Planarity :  0.004   0.033   2896
  Dihedral  :  8.145  61.576   2432
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 16.10 %
    Favored  : 81.05 %
  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:  0.90 (0.18), residues: 2060
  helix:  0.76 (0.18), residues: 764
  sheet:  1.40 (0.27), residues: 348
  loop :  0.30 (0.20), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 125 
 TYR   0.004   0.001   TYR A 216 
 PHE   0.006   0.001   PHE A 443 
 TRP   0.011   0.001   TRP D 176 
 HIS   0.006   0.001   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (16540)
  covalent geometry    : angle       0.52433 (22492)
  hydrogen bonds       : bond        0.03968 (  740)
  hydrogen bonds       : angle       4.69472 ( 2052)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 204
  time to evaluate  : 0.579 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7818 (mpt180)
REVERT: A  218 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.7331 (p0)
REVERT: A  240 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6448 (mm-30)
REVERT: A  350 MET cc_start: 0.8848 (ttm) cc_final: 0.8540 (ttp)
REVERT: A  437 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7624 (tm-30)
REVERT: B   79 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7838 (mpt180)
REVERT: B  218 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7333 (p0)
REVERT: B  240 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6453 (mm-30)
REVERT: B  350 MET cc_start: 0.8841 (ttm) cc_final: 0.8530 (ttp)
REVERT: B  437 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7595 (tm-30)
REVERT: C   79 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7811 (mpt180)
REVERT: C  218 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7327 (p0)
REVERT: C  240 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6449 (mm-30)
REVERT: C  350 MET cc_start: 0.8836 (ttm) cc_final: 0.8529 (ttp)
REVERT: C  437 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7610 (tm-30)
REVERT: D   79 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7874 (mpt180)
REVERT: D  218 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7327 (p0)
REVERT: D  240 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6454 (mm-30)
REVERT: D  350 MET cc_start: 0.8842 (ttm) cc_final: 0.8532 (ttp)
REVERT: D  437 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7595 (tm-30)
  outliers start: 50
  outliers final: 21
  residues processed: 230
  average time/residue: 0.5989
  time to fit residues: 151.7584
Evaluate side-chains
  229 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 192
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue  218 ASP
Chi-restraints excluded: chain B residue  238 CYS
Chi-restraints excluded: chain B residue  240 GLU
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  437 GLU
Chi-restraints excluded: chain B residue  489 THR
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  218 ASP
Chi-restraints excluded: chain C residue  238 CYS
Chi-restraints excluded: chain C residue  240 GLU
Chi-restraints excluded: chain C residue  264 LEU
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  437 GLU
Chi-restraints excluded: chain C residue  489 THR
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  218 ASP
Chi-restraints excluded: chain D residue  238 CYS
Chi-restraints excluded: chain D residue  240 GLU
Chi-restraints excluded: chain D residue  264 LEU
Chi-restraints excluded: chain D residue  370 SER
Chi-restraints excluded: chain D residue  398 VAL
Chi-restraints excluded: chain D residue  437 GLU
Chi-restraints excluded: chain D residue  489 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 106 optimal weight:    0.9980
   chunk 136 optimal weight:    0.6980
   chunk 139 optimal weight:    3.9990
   chunk 130 optimal weight:    0.5980
   chunk 171 optimal weight:    6.9990
   chunk 101 optimal weight:    0.8980
   chunk 61 optimal weight:    8.9990
   chunk 119 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 45 optimal weight:   10.0000
   chunk 39 optimal weight:    6.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
B 256 ASN
C 256 ASN
D 256 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.161420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.141873 restraints weight = 54509.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 2.60
r_work: 0.3463 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3469
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3469
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  16540  Z= 0.142
  Angle     :  0.549   7.258  22492  Z= 0.290
  Chirality :  0.043   0.125   2544
  Planarity :  0.004   0.033   2896
  Dihedral  :  8.301  61.072   2432
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 16.21 %
    Favored  : 81.05 %
  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:  0.81 (0.18), residues: 2060
  helix:  0.67 (0.18), residues: 768
  sheet:  1.07 (0.27), residues: 352
  loop :  0.40 (0.20), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 125 
 TYR   0.005   0.001   TYR C 505 
 PHE   0.007   0.001   PHE A 443 
 TRP   0.010   0.001   TRP A 176 
 HIS   0.006   0.001   HIS D 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (16540)
  covalent geometry    : angle       0.54871 (22492)
  hydrogen bonds       : bond        0.04421 (  740)
  hydrogen bonds       : angle       4.74188 ( 2052)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 185
  time to evaluate  : 0.426 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7729 (mpt180)
REVERT: A  218 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7078 (p0)
REVERT: A  240 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6166 (mm-30)
REVERT: A  350 MET cc_start: 0.8745 (ttm) cc_final: 0.8334 (ttp)
REVERT: A  437 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7512 (tm-30)
REVERT: B   79 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7723 (mpt180)
REVERT: B  218 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7076 (p0)
REVERT: B  240 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6178 (mm-30)
REVERT: B  350 MET cc_start: 0.8752 (ttm) cc_final: 0.8341 (ttp)
REVERT: B  437 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7509 (tm-30)
REVERT: C   79 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7732 (mpt180)
REVERT: C  218 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.7074 (p0)
REVERT: C  240 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6169 (mm-30)
REVERT: C  350 MET cc_start: 0.8747 (ttm) cc_final: 0.8336 (ttp)
REVERT: C  437 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7516 (tm-30)
REVERT: D   79 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7727 (mpt180)
REVERT: D  218 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7080 (p0)
REVERT: D  240 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6166 (mm-30)
REVERT: D  350 MET cc_start: 0.8752 (ttm) cc_final: 0.8342 (ttp)
REVERT: D  437 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7512 (tm-30)
  outliers start: 48
  outliers final: 21
  residues processed: 213
  average time/residue: 0.6211
  time to fit residues: 144.8789
Evaluate side-chains
  221 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 184
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue  218 ASP
Chi-restraints excluded: chain B residue  238 CYS
Chi-restraints excluded: chain B residue  240 GLU
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  437 GLU
Chi-restraints excluded: chain B residue  489 THR
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  218 ASP
Chi-restraints excluded: chain C residue  238 CYS
Chi-restraints excluded: chain C residue  240 GLU
Chi-restraints excluded: chain C residue  264 LEU
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  437 GLU
Chi-restraints excluded: chain C residue  489 THR
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  218 ASP
Chi-restraints excluded: chain D residue  238 CYS
Chi-restraints excluded: chain D residue  240 GLU
Chi-restraints excluded: chain D residue  264 LEU
Chi-restraints excluded: chain D residue  370 SER
Chi-restraints excluded: chain D residue  398 VAL
Chi-restraints excluded: chain D residue  437 GLU
Chi-restraints excluded: chain D residue  489 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 160 optimal weight:    0.6980
   chunk 141 optimal weight:    8.9990
   chunk 178 optimal weight:    0.1980
   chunk 188 optimal weight:    7.9990
   chunk 175 optimal weight:    2.9990
   chunk 167 optimal weight:    3.9990
   chunk 182 optimal weight:    5.9990
   chunk 172 optimal weight:    0.9990
   chunk 71 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.5786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.159640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.139646 restraints weight = 43132.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 2.50
r_work: 0.3449 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3332 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3334
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3334 r_free = 0.3334    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3334 r_free = 0.3334    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3334
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.2290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  16540  Z= 0.181
  Angle     :  0.598   7.944  22492  Z= 0.316
  Chirality :  0.045   0.136   2544
  Planarity :  0.004   0.035   2896
  Dihedral  :  8.554  59.969   2432
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 16.27 %
    Favored  : 80.82 %
  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:  0.61 (0.18), residues: 2060
  helix:  0.42 (0.18), residues: 780
  sheet:  1.02 (0.25), residues: 392
  loop :  0.30 (0.20), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 125 
 TYR   0.007   0.001   TYR A 505 
 PHE   0.010   0.002   PHE B 443 
 TRP   0.010   0.002   TRP D 176 
 HIS   0.006   0.001   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 (16540)
  covalent geometry    : angle       0.59823 (22492)
  hydrogen bonds       : bond        0.04977 (  740)
  hydrogen bonds       : angle       4.88063 ( 2052)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 180
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7843 (mpt180)
REVERT: A  194 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.7069 (mm-30)
REVERT: A  218 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7246 (p0)
REVERT: A  240 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6365 (mm-30)
REVERT: A  350 MET cc_start: 0.8883 (ttm) cc_final: 0.8520 (ttp)
REVERT: A  437 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7763 (tm-30)
REVERT: B   79 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7838 (mpt180)
REVERT: B  194 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7062 (mm-30)
REVERT: B  218 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7247 (p0)
REVERT: B  240 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6365 (mm-30)
REVERT: B  350 MET cc_start: 0.8883 (ttm) cc_final: 0.8518 (ttp)
REVERT: B  437 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7766 (tm-30)
REVERT: C   79 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7831 (mpt180)
REVERT: C  194 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7076 (mm-30)
REVERT: C  218 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7246 (p0)
REVERT: C  240 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6379 (mm-30)
REVERT: C  350 MET cc_start: 0.8885 (ttm) cc_final: 0.8517 (ttp)
REVERT: C  437 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7766 (tm-30)
REVERT: D   79 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7836 (mpt180)
REVERT: D  218 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7250 (p0)
REVERT: D  240 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6377 (mm-30)
REVERT: D  350 MET cc_start: 0.8888 (ttm) cc_final: 0.8523 (ttp)
REVERT: D  437 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7756 (tm-30)
  outliers start: 51
  outliers final: 28
  residues processed: 207
  average time/residue: 0.5751
  time to fit residues: 131.0324
Evaluate side-chains
  223 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 176
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue  187 MET
Chi-restraints excluded: chain B residue  194 GLU
Chi-restraints excluded: chain B residue  218 ASP
Chi-restraints excluded: chain B residue  238 CYS
Chi-restraints excluded: chain B residue  240 GLU
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  437 GLU
Chi-restraints excluded: chain B residue  489 THR
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  187 MET
Chi-restraints excluded: chain C residue  194 GLU
Chi-restraints excluded: chain C residue  218 ASP
Chi-restraints excluded: chain C residue  238 CYS
Chi-restraints excluded: chain C residue  240 GLU
Chi-restraints excluded: chain C residue  264 LEU
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  437 GLU
Chi-restraints excluded: chain C residue  489 THR
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  187 MET
Chi-restraints excluded: chain D residue  218 ASP
Chi-restraints excluded: chain D residue  238 CYS
Chi-restraints excluded: chain D residue  240 GLU
Chi-restraints excluded: chain D residue  264 LEU
Chi-restraints excluded: chain D residue  370 SER
Chi-restraints excluded: chain D residue  398 VAL
Chi-restraints excluded: chain D residue  437 GLU
Chi-restraints excluded: chain D residue  489 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 199 optimal weight:    3.9990
   chunk 112 optimal weight:    7.9990
   chunk 190 optimal weight:    0.0970
   chunk 203 optimal weight:    0.0370
   chunk 151 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   chunk 122 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 22 optimal weight:    0.8980
   chunk 172 optimal weight:    3.9990
   chunk 166 optimal weight:    0.9990
   overall best weight:    0.5858

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.164290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.144727 restraints weight = 53091.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 2.58
r_work: 0.3494 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3502
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3502 r_free = 0.3502    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3502 r_free = 0.3502    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3502
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  16540  Z= 0.117
  Angle     :  0.521   6.217  22492  Z= 0.275
  Chirality :  0.042   0.126   2544
  Planarity :  0.004   0.032   2896
  Dihedral  :  8.098  60.560   2432
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 17.52 %
    Favored  : 80.59 %
  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:  0.97 (0.18), residues: 2060
  helix:  0.79 (0.18), residues: 768
  sheet:  1.20 (0.27), residues: 356
  loop :  0.48 (0.20), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 125 
 TYR   0.004   0.001   TYR B 216 
 PHE   0.006   0.001   PHE D 552 
 TRP   0.012   0.001   TRP D 176 
 HIS   0.006   0.001   HIS C 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (16540)
  covalent geometry    : angle       0.52137 (22492)
  hydrogen bonds       : bond        0.03833 (  740)
  hydrogen bonds       : angle       4.69401 ( 2052)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 184
  time to evaluate  : 0.441 
Fit side-chains
REVERT: A  240 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6098 (mm-30)
REVERT: A  291 LYS cc_start: 0.7622 (mttp) cc_final: 0.7410 (mttp)
REVERT: A  350 MET cc_start: 0.8760 (ttm) cc_final: 0.8353 (ttp)
REVERT: A  437 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7457 (tm-30)
REVERT: A  490 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7314 (mp0)
REVERT: B  240 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6106 (mm-30)
REVERT: B  291 LYS cc_start: 0.7618 (mttp) cc_final: 0.7406 (mttp)
REVERT: B  350 MET cc_start: 0.8764 (ttm) cc_final: 0.8357 (ttp)
REVERT: B  437 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7459 (tm-30)
REVERT: B  490 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7316 (mp0)
REVERT: C  240 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6101 (mm-30)
REVERT: C  291 LYS cc_start: 0.7622 (mttp) cc_final: 0.7410 (mttp)
REVERT: C  350 MET cc_start: 0.8761 (ttm) cc_final: 0.8355 (ttp)
REVERT: C  437 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7461 (tm-30)
REVERT: C  490 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7314 (mp0)
REVERT: D  240 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6109 (mm-30)
REVERT: D  291 LYS cc_start: 0.7617 (mttp) cc_final: 0.7405 (mttp)
REVERT: D  350 MET cc_start: 0.8763 (ttm) cc_final: 0.8357 (ttp)
REVERT: D  437 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7461 (tm-30)
REVERT: D  490 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7313 (mp0)
  outliers start: 33
  outliers final: 17
  residues processed: 205
  average time/residue: 0.6557
  time to fit residues: 147.6247
Evaluate side-chains
  201 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 172
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain B residue  240 GLU
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  437 GLU
Chi-restraints excluded: chain B residue  489 THR
Chi-restraints excluded: chain B residue  490 GLU
Chi-restraints excluded: chain C residue  240 GLU
Chi-restraints excluded: chain C residue  264 LEU
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  437 GLU
Chi-restraints excluded: chain C residue  489 THR
Chi-restraints excluded: chain C residue  490 GLU
Chi-restraints excluded: chain D residue  240 GLU
Chi-restraints excluded: chain D residue  264 LEU
Chi-restraints excluded: chain D residue  370 SER
Chi-restraints excluded: chain D residue  398 VAL
Chi-restraints excluded: chain D residue  437 GLU
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  490 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 121 optimal weight:    0.9980
   chunk 108 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 166 optimal weight:    6.9990
   chunk 177 optimal weight:    0.9990
   chunk 100 optimal weight:    3.9990
   chunk 173 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 193 optimal weight:    4.9990
   chunk 79 optimal weight:    0.8980
   overall best weight:    1.1584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.160839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.141350 restraints weight = 50593.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 2.55
r_work: 0.3460 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3463
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3463 r_free = 0.3463    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3463 r_free = 0.3463    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3463
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16540  Z= 0.151
  Angle     :  0.559   7.356  22492  Z= 0.295
  Chirality :  0.043   0.127   2544
  Planarity :  0.004   0.033   2896
  Dihedral  :  8.341  61.218   2432
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 17.58 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.18), residues: 2060
  helix:  0.69 (0.18), residues: 768
  sheet:  1.08 (0.27), residues: 352
  loop :  0.46 (0.20), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 227 
 TYR   0.006   0.001   TYR A 505 
 PHE   0.008   0.001   PHE A 443 
 TRP   0.009   0.001   TRP D 176 
 HIS   0.006   0.001   HIS D 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (16540)
  covalent geometry    : angle       0.55888 (22492)
  hydrogen bonds       : bond        0.04536 (  740)
  hydrogen bonds       : angle       4.76638 ( 2052)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5524.09 seconds
wall clock time: 95 minutes 1.63 seconds (5701.63 seconds total)