Starting phenix.real_space_refine
on Tue Nov 18 20:45:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6bo5_7119/11_2025/6bo5_7119.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6bo5_7119/11_2025/6bo5_7119.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6bo5_7119/11_2025/6bo5_7119.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6bo5_7119/11_2025/6bo5_7119.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6bo5_7119/11_2025/6bo5_7119.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6bo5_7119/11_2025/6bo5_7119.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      96      5.16       5
     C   11280      2.51       5
     N    2900      2.21       5
     O    2960      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17236
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4309
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 557, 4309
          Classifications: {'peptide': 557}
          Incomplete info: {'truncation_to_alanine': 58}
          Link IDs: {'CIS': 3, 'PTRANS': 18, 'TRANS': 535}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 205
          Unresolved non-hydrogen angles: 256
          Unresolved non-hydrogen dihedrals: 161
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 5, 'PHE:plan': 1, 'GLN:plan1': 6, 'GLU:plan': 6, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 110
  Restraints were copied for chains:
    B, D, C
  Time building chain proxies: 4.06, per 1000 atoms: 0.24
  Number of scatterers: 17236
  At special positions: 0
  Unit cell: (136.53, 136.53, 110.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      96     16.00
     O    2960      8.00
     N    2900      7.00
     C   11280      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: 1.47
  Conformation dependent library (CDL) restraints added in 770.0 milliseconds
  

  4392 Ramachandran restraints generated.
    2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4192

  Finding SS restraints...
    Secondary structure from input PDB file:
      96 helices and 4 sheets defined
      59.3% alpha, 1.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 78 through 87
    Processing helix  chain 'A' and resid 119 through 127
    Processing helix  chain 'A' and resid 135 through 143
      removed outlier: 3.895A  pdb=" N   LEU A 139 " --> pdb=" O   CYS A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 174
      removed outlier: 3.994A  pdb=" N   ILE A 170 " --> pdb=" O   SER A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 183
    Processing helix  chain 'A' and resid 212 through 220
      removed outlier: 4.294A  pdb=" N   THR A 220 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 230
    Processing helix  chain 'A' and resid 248 through 256
    Processing helix  chain 'A' and resid 260 through 279
    Processing helix  chain 'A' and resid 297 through 306
    Processing helix  chain 'A' and resid 307 through 316
    Processing helix  chain 'A' and resid 357 through 362
    Processing helix  chain 'A' and resid 370 through 374
      removed outlier: 4.053A  pdb=" N   VAL A 373 " --> pdb=" O   HIS A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 387
    Processing helix  chain 'A' and resid 389 through 392
    Processing helix  chain 'A' and resid 393 through 413
    Processing helix  chain 'A' and resid 428 through 460
      removed outlier: 3.598A  pdb=" N   SER A 432 " --> pdb=" O   THR A 428 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   TYR A 447 " --> pdb=" O   LEU A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 492
      removed outlier: 4.171A  pdb=" N   ILE A 474 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   LEU A 475 " --> pdb=" O   TYR A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 513
      removed outlier: 4.130A  pdb=" N   LEU A 500 " --> pdb=" O   TRP A 496 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   LEU A 513 " --> pdb=" O   TRP A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 536
    Processing helix  chain 'A' and resid 536 through 557
      removed outlier: 3.547A  pdb=" N   PHE A 540 " --> pdb=" O   ASP A 536 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL A 556 " --> pdb=" O   ALA A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 602
    Processing helix  chain 'A' and resid 623 through 649
    Processing helix  chain 'A' and resid 651 through 675
      removed outlier: 4.289A  pdb=" N   ASN A 655 " --> pdb=" O   HIS A 651 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   TRP A 657 " --> pdb=" O   ALA A 653 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   LYS A 661 " --> pdb=" O   TRP A 657 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ASN A 673 " --> pdb=" O   LEU A 669 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   TYR A 675 " --> pdb=" O   MET A 671 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 87
    Processing helix  chain 'B' and resid 119 through 127
    Processing helix  chain 'B' and resid 135 through 143
      removed outlier: 3.895A  pdb=" N   LEU B 139 " --> pdb=" O   CYS B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 174
      removed outlier: 3.993A  pdb=" N   ILE B 170 " --> pdb=" O   SER B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 183
    Processing helix  chain 'B' and resid 212 through 220
      removed outlier: 4.295A  pdb=" N   THR B 220 " --> pdb=" O   LEU B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 230
    Processing helix  chain 'B' and resid 248 through 256
    Processing helix  chain 'B' and resid 260 through 279
    Processing helix  chain 'B' and resid 297 through 306
    Processing helix  chain 'B' and resid 307 through 316
    Processing helix  chain 'B' and resid 357 through 362
    Processing helix  chain 'B' and resid 370 through 374
      removed outlier: 4.053A  pdb=" N   VAL B 373 " --> pdb=" O   HIS B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 375 through 387
    Processing helix  chain 'B' and resid 389 through 392
    Processing helix  chain 'B' and resid 393 through 413
    Processing helix  chain 'B' and resid 428 through 460
      removed outlier: 3.598A  pdb=" N   SER B 432 " --> pdb=" O   THR B 428 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   TYR B 447 " --> pdb=" O   LEU B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 470 through 492
      removed outlier: 4.171A  pdb=" N   ILE B 474 " --> pdb=" O   SER B 470 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   LEU B 475 " --> pdb=" O   TYR B 471 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 513
      removed outlier: 4.130A  pdb=" N   LEU B 500 " --> pdb=" O   TRP B 496 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   LEU B 513 " --> pdb=" O   TRP B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 521 through 536
    Processing helix  chain 'B' and resid 536 through 557
      removed outlier: 3.548A  pdb=" N   PHE B 540 " --> pdb=" O   ASP B 536 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL B 556 " --> pdb=" O   ALA B 552 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 596 through 602
    Processing helix  chain 'B' and resid 623 through 649
    Processing helix  chain 'B' and resid 651 through 675
      removed outlier: 4.289A  pdb=" N   ASN B 655 " --> pdb=" O   HIS B 651 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   TRP B 657 " --> pdb=" O   ALA B 653 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   LYS B 661 " --> pdb=" O   TRP B 657 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ASN B 673 " --> pdb=" O   LEU B 669 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   TYR B 675 " --> pdb=" O   MET B 671 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 79 through 87
    Processing helix  chain 'D' and resid 119 through 127
    Processing helix  chain 'D' and resid 135 through 143
      removed outlier: 3.894A  pdb=" N   LEU D 139 " --> pdb=" O   CYS D 135 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 166 through 174
      removed outlier: 3.994A  pdb=" N   ILE D 170 " --> pdb=" O   SER D 166 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 177 through 183
    Processing helix  chain 'D' and resid 212 through 220
      removed outlier: 4.295A  pdb=" N   THR D 220 " --> pdb=" O   LEU D 216 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 222 through 230
    Processing helix  chain 'D' and resid 248 through 256
    Processing helix  chain 'D' and resid 260 through 279
    Processing helix  chain 'D' and resid 297 through 306
    Processing helix  chain 'D' and resid 307 through 316
    Processing helix  chain 'D' and resid 357 through 362
    Processing helix  chain 'D' and resid 370 through 374
      removed outlier: 4.053A  pdb=" N   VAL D 373 " --> pdb=" O   HIS D 370 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 375 through 387
    Processing helix  chain 'D' and resid 389 through 392
    Processing helix  chain 'D' and resid 393 through 413
    Processing helix  chain 'D' and resid 428 through 460
      removed outlier: 3.598A  pdb=" N   SER D 432 " --> pdb=" O   THR D 428 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   TYR D 447 " --> pdb=" O   LEU D 443 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 470 through 492
      removed outlier: 4.171A  pdb=" N   ILE D 474 " --> pdb=" O   SER D 470 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   LEU D 475 " --> pdb=" O   TYR D 471 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 496 through 513
      removed outlier: 4.130A  pdb=" N   LEU D 500 " --> pdb=" O   TRP D 496 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   LEU D 513 " --> pdb=" O   TRP D 509 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 521 through 536
    Processing helix  chain 'D' and resid 536 through 557
      removed outlier: 3.548A  pdb=" N   PHE D 540 " --> pdb=" O   ASP D 536 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL D 556 " --> pdb=" O   ALA D 552 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 596 through 602
    Processing helix  chain 'D' and resid 623 through 649
    Processing helix  chain 'D' and resid 651 through 675
      removed outlier: 4.289A  pdb=" N   ASN D 655 " --> pdb=" O   HIS D 651 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   TRP D 657 " --> pdb=" O   ALA D 653 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   LYS D 661 " --> pdb=" O   TRP D 657 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ASN D 673 " --> pdb=" O   LEU D 669 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   TYR D 675 " --> pdb=" O   MET D 671 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 87
    Processing helix  chain 'C' and resid 119 through 127
    Processing helix  chain 'C' and resid 135 through 143
      removed outlier: 3.896A  pdb=" N   LEU C 139 " --> pdb=" O   CYS C 135 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 166 through 174
      removed outlier: 3.994A  pdb=" N   ILE C 170 " --> pdb=" O   SER C 166 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 177 through 183
    Processing helix  chain 'C' and resid 212 through 220
      removed outlier: 4.294A  pdb=" N   THR C 220 " --> pdb=" O   LEU C 216 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 230
    Processing helix  chain 'C' and resid 248 through 256
    Processing helix  chain 'C' and resid 260 through 279
    Processing helix  chain 'C' and resid 297 through 306
    Processing helix  chain 'C' and resid 307 through 316
    Processing helix  chain 'C' and resid 357 through 362
    Processing helix  chain 'C' and resid 370 through 374
      removed outlier: 4.053A  pdb=" N   VAL C 373 " --> pdb=" O   HIS C 370 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 375 through 387
    Processing helix  chain 'C' and resid 389 through 392
    Processing helix  chain 'C' and resid 393 through 413
    Processing helix  chain 'C' and resid 428 through 460
      removed outlier: 3.598A  pdb=" N   SER C 432 " --> pdb=" O   THR C 428 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   TYR C 447 " --> pdb=" O   LEU C 443 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 470 through 492
      removed outlier: 4.171A  pdb=" N   ILE C 474 " --> pdb=" O   SER C 470 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   LEU C 475 " --> pdb=" O   TYR C 471 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 496 through 513
      removed outlier: 4.130A  pdb=" N   LEU C 500 " --> pdb=" O   TRP C 496 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   LEU C 513 " --> pdb=" O   TRP C 509 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 521 through 536
    Processing helix  chain 'C' and resid 536 through 557
      removed outlier: 3.547A  pdb=" N   PHE C 540 " --> pdb=" O   ASP C 536 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL C 556 " --> pdb=" O   ALA C 552 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 596 through 602
    Processing helix  chain 'C' and resid 623 through 649
    Processing helix  chain 'C' and resid 651 through 675
      removed outlier: 4.289A  pdb=" N   ASN C 655 " --> pdb=" O   HIS C 651 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   TRP C 657 " --> pdb=" O   ALA C 653 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   LYS C 661 " --> pdb=" O   TRP C 657 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ASN C 673 " --> pdb=" O   LEU C 669 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   TYR C 675 " --> pdb=" O   MET C 671 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 331
      removed outlier: 3.538A  pdb=" N   LEU A 689 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 331
      removed outlier: 3.537A  pdb=" N   LEU B 689 " --> pdb=" O   SER B 341 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 329 through 331
      removed outlier: 3.537A  pdb=" N   LEU D 689 " --> pdb=" O   SER D 341 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 329 through 331
      removed outlier: 3.537A  pdb=" N   LEU C 689 " --> pdb=" O   SER C 341 " (cutoff:3.500A)

    897 hydrogen bonds defined for protein.
    2655 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: 2.44

  Time building geometry restraints manager: 1.96 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 5355
        1.34 -     1.46: 3620
        1.46 -     1.58: 8533
        1.58 -     1.69: 0
        1.69 -     1.81: 148
  Bond restraints: 17656
  Sorted by residual:
  bond pdb=" C   GLN B 324 "
       pdb=" N   PRO B 325 "
    ideal  model  delta    sigma   weight residual
    1.334  1.414 -0.080 2.34e-02 1.83e+03 1.16e+01
  bond pdb=" C   GLN D 324 "
       pdb=" N   PRO D 325 "
    ideal  model  delta    sigma   weight residual
    1.334  1.414 -0.080 2.34e-02 1.83e+03 1.16e+01
  bond pdb=" C   GLN A 324 "
       pdb=" N   PRO A 325 "
    ideal  model  delta    sigma   weight residual
    1.334  1.413 -0.079 2.34e-02 1.83e+03 1.15e+01
  bond pdb=" C   GLN C 324 "
       pdb=" N   PRO C 325 "
    ideal  model  delta    sigma   weight residual
    1.334  1.413 -0.079 2.34e-02 1.83e+03 1.15e+01
  bond pdb=" CA  PHE A 519 "
       pdb=" CB  PHE A 519 "
    ideal  model  delta    sigma   weight residual
    1.521  1.564 -0.043 1.48e-02 4.57e+03 8.42e+00
  ... (remaining 17651 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.30: 23607
        3.30 -     6.60: 324
        6.60 -     9.90: 69
        9.90 -    13.21: 4
       13.21 -    16.51: 8
  Bond angle restraints: 24012
  Sorted by residual:
  angle pdb=" N   VAL B 621 "
        pdb=" CA  VAL B 621 "
        pdb=" C   VAL B 621 "
      ideal   model   delta    sigma   weight residual
     111.09  125.63  -14.54 1.25e+00 6.40e-01 1.35e+02
  angle pdb=" N   VAL C 621 "
        pdb=" CA  VAL C 621 "
        pdb=" C   VAL C 621 "
      ideal   model   delta    sigma   weight residual
     111.09  125.63  -14.54 1.25e+00 6.40e-01 1.35e+02
  angle pdb=" N   VAL A 621 "
        pdb=" CA  VAL A 621 "
        pdb=" C   VAL A 621 "
      ideal   model   delta    sigma   weight residual
     111.09  125.63  -14.54 1.25e+00 6.40e-01 1.35e+02
  angle pdb=" N   VAL D 621 "
        pdb=" CA  VAL D 621 "
        pdb=" C   VAL D 621 "
      ideal   model   delta    sigma   weight residual
     111.09  125.63  -14.54 1.25e+00 6.40e-01 1.35e+02
  angle pdb=" N   VAL B 390 "
        pdb=" CA  VAL B 390 "
        pdb=" C   VAL B 390 "
      ideal   model   delta    sigma   weight residual
     112.35  102.48    9.87 1.41e+00 5.03e-01 4.90e+01
  ... (remaining 24007 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.26: 9644
       19.26 -    38.53: 524
       38.53 -    57.79: 92
       57.79 -    77.06: 16
       77.06 -    96.32: 4
  Dihedral angle restraints: 10280
    sinusoidal: 3792
      harmonic: 6488
  Sorted by residual:
  dihedral pdb=" CA  HIS B 363 "
           pdb=" C   HIS B 363 "
           pdb=" N   CYS B 364 "
           pdb=" CA  CYS B 364 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -83.68  -96.32     0      5.00e+00 4.00e-02 3.71e+02
  dihedral pdb=" CA  HIS A 363 "
           pdb=" C   HIS A 363 "
           pdb=" N   CYS A 364 "
           pdb=" CA  CYS A 364 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -83.70  -96.30     0      5.00e+00 4.00e-02 3.71e+02
  dihedral pdb=" CA  HIS C 363 "
           pdb=" C   HIS C 363 "
           pdb=" N   CYS C 364 "
           pdb=" CA  CYS C 364 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -83.73  -96.27     0      5.00e+00 4.00e-02 3.71e+02
  ... (remaining 10277 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 2504
       0.092 -    0.184: 244
       0.184 -    0.276: 9
       0.276 -    0.368: 3
       0.368 -    0.461: 4
  Chirality restraints: 2764
  Sorted by residual:
  chirality pdb=" CA  VAL D 621 "
            pdb=" N   VAL D 621 "
            pdb=" C   VAL D 621 "
            pdb=" CB  VAL D 621 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.98    0.46 2.00e-01 2.50e+01 5.30e+00
  chirality pdb=" CA  VAL A 621 "
            pdb=" N   VAL A 621 "
            pdb=" C   VAL A 621 "
            pdb=" CB  VAL A 621 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.98    0.46 2.00e-01 2.50e+01 5.27e+00
  chirality pdb=" CA  VAL C 621 "
            pdb=" N   VAL C 621 "
            pdb=" C   VAL C 621 "
            pdb=" CB  VAL C 621 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.98    0.46 2.00e-01 2.50e+01 5.27e+00
  ... (remaining 2761 not shown)

  Planarity restraints: 2984
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE D 519 "   -0.013 2.00e-02 2.50e+03   2.61e-02 6.82e+00
        pdb=" C   PHE D 519 "    0.045 2.00e-02 2.50e+03
        pdb=" O   PHE D 519 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   GLN D 520 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE C 519 "   -0.013 2.00e-02 2.50e+03   2.61e-02 6.82e+00
        pdb=" C   PHE C 519 "    0.045 2.00e-02 2.50e+03
        pdb=" O   PHE C 519 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   GLN C 520 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 519 "    0.013 2.00e-02 2.50e+03   2.59e-02 6.69e+00
        pdb=" C   PHE A 519 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   PHE A 519 "    0.017 2.00e-02 2.50e+03
        pdb=" N   GLN A 520 "    0.015 2.00e-02 2.50e+03
  ... (remaining 2981 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 4674
        2.80 -     3.33: 16020
        3.33 -     3.85: 27979
        3.85 -     4.38: 31364
        4.38 -     4.90: 51483
  Nonbonded interactions: 131520
  Sorted by model distance:
  nonbonded pdb=" O   MET C 404 "
            pdb=" OG1 THR C 408 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   MET D 404 "
            pdb=" OG1 THR D 408 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   MET B 404 "
            pdb=" OG1 THR B 408 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   MET A 404 "
            pdb=" OG1 THR A 408 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OE1 GLN C 479 "
            pdb=" ND2 ASN C 511 "
     model   vdw
     2.295 3.120
  ... (remaining 131515 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'D'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.700
  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:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     15.900
  Find NCS groups from input model:        0.150
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080  17656  Z= 0.231
  Angle     :  1.082  16.507  24012  Z= 0.587
  Chirality :  0.055   0.461   2764
  Planarity :  0.007   0.064   2984
  Dihedral  : 12.892  96.321   6088
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  9.11 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  :  6.67 %
    Favored  : 91.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.56 %
    Twisted Proline : 0.00 %
    Twisted General : 2.24 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.44 (0.12), residues: 2196
  helix: -3.76 (0.08), residues: 1188
  sheet: -2.75 (0.58), residues: 40
  loop : -3.32 (0.16), residues: 968

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 328 
 TYR   0.032   0.003   TYR A 323 
 PHE   0.026   0.003   PHE B 209 
 TRP   0.033   0.002   TRP C 496 
 HIS   0.007   0.002   HIS D 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (17656)
  covalent geometry    : angle       1.08184 (24012)
  hydrogen bonds       : bond        0.12807 (  897)
  hydrogen bonds       : angle      11.99190 ( 2655)

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

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

  4392 Ramachandran restraints generated.
    2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4392 Ramachandran restraints generated.
    2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  380 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 348
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  433 MET cc_start: 0.6313 (ttp) cc_final: 0.6038 (mtp)
REVERT: A  634 TYR cc_start: 0.7375 (t80) cc_final: 0.6973 (t80)
REVERT: B  433 MET cc_start: 0.6309 (ttp) cc_final: 0.6023 (mtp)
REVERT: D  433 MET cc_start: 0.6313 (ttp) cc_final: 0.6025 (mtp)
REVERT: D  529 ILE cc_start: 0.8368 (pp) cc_final: 0.8155 (pt)
REVERT: C  433 MET cc_start: 0.6311 (ttp) cc_final: 0.6024 (mtp)
REVERT: C  529 ILE cc_start: 0.8365 (pp) cc_final: 0.8153 (pt)
  outliers start: 32
  outliers final: 0
  residues processed: 376
  average time/residue: 0.1762
  time to fit residues: 92.5889
Evaluate side-chains
  168 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 216 optimal weight:    8.9990
   chunk 98 optimal weight:    4.9990
   chunk 194 optimal weight:    7.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.3980
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    5.9990
   chunk 200 optimal weight:    0.1980
   chunk 212 optimal weight:    6.9990
   overall best weight:    2.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 251 HIS
A 259 ASN
A 286 GLN
A 368 ASN
A 530 GLN
B 251 HIS
B 259 ASN
B 286 GLN
B 368 ASN
B 530 GLN
D 251 HIS
D 259 ASN
D 286 GLN
D 368 ASN
D 530 GLN
D 655 ASN
C 251 HIS
C 259 ASN
C 286 GLN
C 368 ASN
C 530 GLN

Total number of N/Q/H flips: 21

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.105956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.097565 restraints weight = 78667.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.098615 restraints weight = 56115.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.099413 restraints weight = 43107.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.099955 restraints weight = 35205.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.100378 restraints weight = 30301.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
moved from start:          0.2793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  17656  Z= 0.158
  Angle     :  0.775  10.412  24012  Z= 0.396
  Chirality :  0.041   0.152   2764
  Planarity :  0.006   0.053   2984
  Dihedral  :  7.784  44.649   2392
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 10.40 %
    Favored  : 85.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.56 %
    Twisted Proline : 0.00 %
    Twisted General : 1.50 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.44 (0.15), residues: 2196
  helix: -1.72 (0.13), residues: 1252
  sheet: -2.74 (0.56), residues: 56
  loop : -3.00 (0.18), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 458 
 TYR   0.025   0.002   TYR D 323 
 PHE   0.024   0.002   PHE B 519 
 TRP   0.020   0.002   TRP A 454 
 HIS   0.004   0.001   HIS C 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (17656)
  covalent geometry    : angle       0.77516 (24012)
  hydrogen bonds       : bond        0.04647 (  897)
  hydrogen bonds       : angle       6.15328 ( 2655)

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

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

  4392 Ramachandran restraints generated.
    2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4392 Ramachandran restraints generated.
    2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 189
  time to evaluate  : 0.706 
Fit side-chains
  outliers start: 68
  outliers final: 29
  residues processed: 245
  average time/residue: 0.1261
  time to fit residues: 47.7842
Evaluate side-chains
  174 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  498 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  375 LEU
Chi-restraints excluded: chain D residue  434 LEU
Chi-restraints excluded: chain D residue  461 LEU
Chi-restraints excluded: chain D residue  488 VAL
Chi-restraints excluded: chain D residue  498 LEU
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  375 LEU
Chi-restraints excluded: chain C residue  434 LEU
Chi-restraints excluded: chain C residue  461 LEU
Chi-restraints excluded: chain C residue  488 VAL
Chi-restraints excluded: chain C residue  498 LEU
Chi-restraints excluded: chain C residue  507 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 215 optimal weight:    6.9990
   chunk 43 optimal weight:   20.0000
   chunk 206 optimal weight:    2.9990
   chunk 98 optimal weight:    7.9990
   chunk 11 optimal weight:    7.9990
   chunk 107 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 148 optimal weight:   10.0000
   chunk 193 optimal weight:    6.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 276 GLN
** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 276 GLN
B 511 ASN
** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 276 GLN
** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 GLN
C 511 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.103551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.095487 restraints weight = 79152.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.096449 restraints weight = 57468.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.097086 restraints weight = 44996.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.097675 restraints weight = 37764.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.098076 restraints weight = 32844.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.3566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  17656  Z= 0.160
  Angle     :  0.744  10.500  24012  Z= 0.376
  Chirality :  0.042   0.145   2764
  Planarity :  0.005   0.049   2984
  Dihedral  :  7.180  36.959   2392
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 14.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 11.95 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.56 %
    Twisted Proline : 0.00 %
    Twisted General : 1.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.40 (0.16), residues: 2196
  helix: -0.74 (0.14), residues: 1280
  sheet: -2.84 (0.55), residues: 56
  loop : -2.78 (0.19), residues: 860

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 392 
 TYR   0.022   0.002   TYR A 525 
 PHE   0.015   0.002   PHE C 207 
 TRP   0.017   0.002   TRP A 496 
 HIS   0.004   0.001   HIS C 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (17656)
  covalent geometry    : angle       0.74441 (24012)
  hydrogen bonds       : bond        0.04256 (  897)
  hydrogen bonds       : angle       5.39705 ( 2655)

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

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

  4392 Ramachandran restraints generated.
    2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4392 Ramachandran restraints generated.
    2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 152
  time to evaluate  : 0.693 
Fit side-chains
REVERT: A  529 ILE cc_start: 0.7930 (pt) cc_final: 0.7118 (pt)
REVERT: A  535 ARG cc_start: 0.7532 (tpp-160) cc_final: 0.7290 (tpp-160)
REVERT: A  640 MET cc_start: 0.7948 (tpt) cc_final: 0.7598 (tpt)
REVERT: A  645 MET cc_start: 0.5734 (mmp) cc_final: 0.5520 (mpp)
REVERT: B  529 ILE cc_start: 0.7883 (pt) cc_final: 0.6982 (pt)
REVERT: B  535 ARG cc_start: 0.7535 (tpp-160) cc_final: 0.7290 (tpp-160)
REVERT: B  640 MET cc_start: 0.7967 (tpt) cc_final: 0.7577 (tpt)
REVERT: D  502 VAL cc_start: 0.7614 (t) cc_final: 0.7411 (t)
REVERT: D  529 ILE cc_start: 0.7897 (pt) cc_final: 0.6986 (pt)
REVERT: D  535 ARG cc_start: 0.7538 (tpp-160) cc_final: 0.7295 (tpp-160)
REVERT: D  640 MET cc_start: 0.7964 (tpt) cc_final: 0.7628 (tpt)
REVERT: C  529 ILE cc_start: 0.7891 (pt) cc_final: 0.6984 (pt)
REVERT: C  535 ARG cc_start: 0.7531 (tpp-160) cc_final: 0.7286 (tpp-160)
REVERT: C  640 MET cc_start: 0.7969 (tpt) cc_final: 0.7603 (tpt)
  outliers start: 46
  outliers final: 34
  residues processed: 189
  average time/residue: 0.1172
  time to fit residues: 36.1894
Evaluate side-chains
  166 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 132
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  375 LEU
Chi-restraints excluded: chain D residue  434 LEU
Chi-restraints excluded: chain D residue  461 LEU
Chi-restraints excluded: chain D residue  488 VAL
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain C residue  128 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  375 LEU
Chi-restraints excluded: chain C residue  434 LEU
Chi-restraints excluded: chain C residue  461 LEU
Chi-restraints excluded: chain C residue  488 VAL
Chi-restraints excluded: chain C residue  507 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 102 optimal weight:    0.0970
   chunk 117 optimal weight:    0.0970
   chunk 113 optimal weight:    9.9990
   chunk 176 optimal weight:    8.9990
   chunk 131 optimal weight:    9.9990
   chunk 180 optimal weight:    0.0040
   chunk 1 optimal weight:    0.4980
   chunk 36 optimal weight:    9.9990
   chunk 147 optimal weight:    6.9990
   chunk 177 optimal weight:    0.5980
   chunk 108 optimal weight:    2.9990
   overall best weight:    0.2588

-------------------------------------------------------------------------------
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 = 0.4120 r_free = 0.4120 target = 0.108767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.101388 restraints weight = 80898.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.102554 restraints weight = 55053.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.103474 restraints weight = 40648.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.104025 restraints weight = 32096.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.104566 restraints weight = 26825.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.4051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.4319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.054  17656  Z= 0.118
  Angle     :  0.681  13.192  24012  Z= 0.335
  Chirality :  0.039   0.145   2764
  Planarity :  0.004   0.050   2984
  Dihedral  :  6.321  38.064   2392
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 13.85 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.56 %
    Twisted Proline : 0.00 %
    Twisted General : 0.75 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.18), residues: 2196
  helix:  0.06 (0.15), residues: 1296
  sheet:  None (None), residues: 0
  loop : -2.40 (0.20), residues: 900

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 392 
 TYR   0.029   0.001   TYR A 525 
 PHE   0.013   0.001   PHE C 551 
 TRP   0.009   0.001   TRP C 676 
 HIS   0.002   0.000   HIS C 438 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 (17656)
  covalent geometry    : angle       0.68088 (24012)
  hydrogen bonds       : bond        0.03766 (  897)
  hydrogen bonds       : angle       4.55936 ( 2655)

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

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

  4392 Ramachandran restraints generated.
    2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4392 Ramachandran restraints generated.
    2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 188
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A  640 MET cc_start: 0.7810 (tpt) cc_final: 0.7346 (tpt)
REVERT: B  640 MET cc_start: 0.7772 (tpt) cc_final: 0.7548 (tpt)
REVERT: D  640 MET cc_start: 0.7663 (tpt) cc_final: 0.7312 (tpt)
REVERT: C  640 MET cc_start: 0.7791 (tpt) cc_final: 0.7283 (tpt)
  outliers start: 38
  outliers final: 21
  residues processed: 215
  average time/residue: 0.1335
  time to fit residues: 43.8407
Evaluate side-chains
  153 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  375 LEU
Chi-restraints excluded: chain D residue  434 LEU
Chi-restraints excluded: chain D residue  461 LEU
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  375 LEU
Chi-restraints excluded: chain C residue  434 LEU
Chi-restraints excluded: chain C residue  461 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 185 optimal weight:   10.0000
   chunk 168 optimal weight:    4.9990
   chunk 124 optimal weight:    8.9990
   chunk 77 optimal weight:    0.0170
   chunk 21 optimal weight:    1.9990
   chunk 94 optimal weight:    5.9990
   chunk 90 optimal weight:    3.9990
   chunk 49 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   chunk 138 optimal weight:    0.9990
   chunk 182 optimal weight:    0.9980
   overall best weight:    1.6024

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

Flipped N/Q/H residues before XYZ refinement:
** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 HIS
** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 HIS
** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 293 HIS
** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 293 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.106992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.099480 restraints weight = 80484.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.100694 restraints weight = 54307.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.101643 restraints weight = 39955.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.102219 restraints weight = 31194.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.102752 restraints weight = 25919.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.4013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7192
moved from start:          0.4550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  17656  Z= 0.116
  Angle     :  0.674  12.443  24012  Z= 0.340
  Chirality :  0.040   0.157   2764
  Planarity :  0.004   0.045   2984
  Dihedral  :  6.074  32.451   2392
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 13.85 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.56 %
    Twisted Proline : 0.00 %
    Twisted General : 0.56 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.18), residues: 2196
  helix:  0.30 (0.15), residues: 1284
  sheet:  None (None), residues: 0
  loop : -2.23 (0.20), residues: 912

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 459 
 TYR   0.021   0.001   TYR D 525 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.008   0.001   TRP C 677 
 HIS   0.009   0.001   HIS B 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (17656)
  covalent geometry    : angle       0.67361 (24012)
  hydrogen bonds       : bond        0.03624 (  897)
  hydrogen bonds       : angle       4.48828 ( 2655)

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

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

  4392 Ramachandran restraints generated.
    2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4392 Ramachandran restraints generated.
    2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 145
  time to evaluate  : 0.848 
Fit side-chains
REVERT: A  619 ARG cc_start: 0.5139 (OUTLIER) cc_final: 0.3584 (mtp180)
REVERT: C  640 MET cc_start: 0.7778 (tpt) cc_final: 0.7528 (tpt)
  outliers start: 57
  outliers final: 36
  residues processed: 194
  average time/residue: 0.1250
  time to fit residues: 38.2206
Evaluate side-chains
  161 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 124
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  619 ARG
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  619 ARG
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  375 LEU
Chi-restraints excluded: chain D residue  434 LEU
Chi-restraints excluded: chain D residue  461 LEU
Chi-restraints excluded: chain D residue  488 VAL
Chi-restraints excluded: chain D residue  619 ARG
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain C residue  128 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  375 LEU
Chi-restraints excluded: chain C residue  434 LEU
Chi-restraints excluded: chain C residue  461 LEU
Chi-restraints excluded: chain C residue  488 VAL
Chi-restraints excluded: chain C residue  619 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 123 optimal weight:   20.0000
   chunk 175 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 172 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 165 optimal weight:   50.0000
   chunk 28 optimal weight:    0.9980
   chunk 133 optimal weight:    2.9990
   chunk 63 optimal weight:   20.0000
   chunk 81 optimal weight:    1.9990
   chunk 183 optimal weight:   20.0000
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 HIS
** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 HIS
** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 293 HIS
** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 293 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.106006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.098768 restraints weight = 80825.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.099878 restraints weight = 55721.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.100771 restraints weight = 41562.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.101293 restraints weight = 32916.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.101809 restraints weight = 27653.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.4698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  17656  Z= 0.123
  Angle     :  0.666  10.090  24012  Z= 0.338
  Chirality :  0.041   0.279   2764
  Planarity :  0.004   0.044   2984
  Dihedral  :  6.023  32.702   2392
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 14.31 %
    Favored  : 82.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.56 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.94 (0.18), residues: 2196
  helix:  0.37 (0.14), residues: 1280
  sheet:  None (None), residues: 0
  loop : -2.08 (0.20), residues: 916

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 392 
 TYR   0.022   0.001   TYR D 525 
 PHE   0.012   0.001   PHE A 199 
 TRP   0.008   0.001   TRP C 677 
 HIS   0.009   0.001   HIS C 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (17656)
  covalent geometry    : angle       0.66560 (24012)
  hydrogen bonds       : bond        0.03686 (  897)
  hydrogen bonds       : angle       4.57775 ( 2655)

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

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

  4392 Ramachandran restraints generated.
    2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4392 Ramachandran restraints generated.
    2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 146
  time to evaluate  : 0.769 
Fit side-chains
REVERT: A  640 MET cc_start: 0.7614 (tpt) cc_final: 0.7232 (tpt)
REVERT: B  502 VAL cc_start: 0.7396 (t) cc_final: 0.7154 (t)
REVERT: B  640 MET cc_start: 0.7508 (tpt) cc_final: 0.7171 (tpt)
REVERT: D  640 MET cc_start: 0.7575 (tpt) cc_final: 0.7200 (tpt)
REVERT: C  502 VAL cc_start: 0.7394 (t) cc_final: 0.7143 (t)
  outliers start: 48
  outliers final: 40
  residues processed: 186
  average time/residue: 0.1207
  time to fit residues: 35.6042
Evaluate side-chains
  162 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 122
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  293 HIS
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  619 ARG
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  293 HIS
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  619 ARG
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  293 HIS
Chi-restraints excluded: chain D residue  375 LEU
Chi-restraints excluded: chain D residue  434 LEU
Chi-restraints excluded: chain D residue  461 LEU
Chi-restraints excluded: chain D residue  619 ARG
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain C residue  128 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  293 HIS
Chi-restraints excluded: chain C residue  375 LEU
Chi-restraints excluded: chain C residue  434 LEU
Chi-restraints excluded: chain C residue  461 LEU
Chi-restraints excluded: chain C residue  477 LEU
Chi-restraints excluded: chain C residue  619 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 152 optimal weight:   10.0000
   chunk 198 optimal weight:    0.0870
   chunk 174 optimal weight:    7.9990
   chunk 132 optimal weight:    6.9990
   chunk 202 optimal weight:    3.9990
   chunk 191 optimal weight:   10.0000
   chunk 125 optimal weight:    3.9990
   chunk 177 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 149 optimal weight:    2.9990
   chunk 121 optimal weight:    6.9990
   overall best weight:    3.6166

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

Flipped N/Q/H residues before XYZ refinement:
** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 HIS
** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 HIS
** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 293 HIS
** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 293 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.104762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.097138 restraints weight = 79674.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.098282 restraints weight = 55682.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.099118 restraints weight = 42232.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.099728 restraints weight = 33863.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.100082 restraints weight = 28516.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7231
moved from start:          0.4744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  17656  Z= 0.153
  Angle     :  0.716  11.459  24012  Z= 0.364
  Chirality :  0.042   0.203   2764
  Planarity :  0.004   0.042   2984
  Dihedral  :  6.121  31.040   2392
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.65 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 14.71 %
    Favored  : 82.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.56 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.05 (0.17), residues: 2196
  helix:  0.23 (0.14), residues: 1280
  sheet:  None (None), residues: 0
  loop : -2.06 (0.20), residues: 916

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 392 
 TYR   0.026   0.002   TYR B 525 
 PHE   0.014   0.001   PHE A 207 
 TRP   0.010   0.001   TRP A 677 
 HIS   0.009   0.001   HIS C 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (17656)
  covalent geometry    : angle       0.71602 (24012)
  hydrogen bonds       : bond        0.03898 (  897)
  hydrogen bonds       : angle       4.73165 ( 2655)

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

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

  4392 Ramachandran restraints generated.
    2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4392 Ramachandran restraints generated.
    2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 134
  time to evaluate  : 0.723 
Fit side-chains
REVERT: A  640 MET cc_start: 0.7651 (tpt) cc_final: 0.7368 (tpt)
  outliers start: 50
  outliers final: 36
  residues processed: 176
  average time/residue: 0.1255
  time to fit residues: 34.8572
Evaluate side-chains
  166 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 130
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  293 HIS
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  619 ARG
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  293 HIS
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  619 ARG
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  293 HIS
Chi-restraints excluded: chain D residue  434 LEU
Chi-restraints excluded: chain D residue  461 LEU
Chi-restraints excluded: chain D residue  477 LEU
Chi-restraints excluded: chain D residue  619 ARG
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain C residue  128 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  293 HIS
Chi-restraints excluded: chain C residue  434 LEU
Chi-restraints excluded: chain C residue  461 LEU
Chi-restraints excluded: chain C residue  477 LEU
Chi-restraints excluded: chain C residue  619 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 144 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 116 optimal weight:    6.9990
   chunk 168 optimal weight:    0.9990
   chunk 117 optimal weight:    0.9980
   chunk 72 optimal weight:   10.0000
   chunk 67 optimal weight:    0.9990
   chunk 189 optimal weight:    0.0870
   chunk 201 optimal weight:    5.9990
   chunk 83 optimal weight:    0.9990
   overall best weight:    0.8164

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

Flipped N/Q/H residues before XYZ refinement:
A 293 HIS
** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 HIS
** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 293 HIS
** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 293 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.107362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.099894 restraints weight = 80190.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.101163 restraints weight = 53080.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.102118 restraints weight = 38638.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.102798 restraints weight = 29896.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.103196 restraints weight = 24343.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7179
moved from start:          0.5035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  17656  Z= 0.114
  Angle     :  0.714  16.726  24012  Z= 0.347
  Chirality :  0.041   0.180   2764
  Planarity :  0.004   0.045   2984
  Dihedral  :  5.808  29.975   2392
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 15.86 %
    Favored  : 82.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.56 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.18), residues: 2196
  helix:  0.55 (0.15), residues: 1268
  sheet:  None (None), residues: 0
  loop : -1.92 (0.20), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 339 
 TYR   0.028   0.001   TYR A 525 
 PHE   0.011   0.001   PHE D 199 
 TRP   0.007   0.001   TRP D 496 
 HIS   0.014   0.001   HIS C 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (17656)
  covalent geometry    : angle       0.71416 (24012)
  hydrogen bonds       : bond        0.03627 (  897)
  hydrogen bonds       : angle       4.47011 ( 2655)

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

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

  4392 Ramachandran restraints generated.
    2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4392 Ramachandran restraints generated.
    2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 132
  time to evaluate  : 0.666 
Fit side-chains
REVERT: A  433 MET cc_start: 0.6285 (ttm) cc_final: 0.5937 (ttp)
REVERT: A  619 ARG cc_start: 0.5450 (OUTLIER) cc_final: 0.3937 (mtp180)
REVERT: A  640 MET cc_start: 0.7613 (tpt) cc_final: 0.7210 (tpt)
REVERT: B  528 MET cc_start: 0.6359 (ppp) cc_final: 0.6153 (pmm)
REVERT: B  619 ARG cc_start: 0.5379 (OUTLIER) cc_final: 0.3864 (mtp180)
REVERT: D  528 MET cc_start: 0.6359 (ppp) cc_final: 0.6128 (pmm)
REVERT: D  619 ARG cc_start: 0.5393 (OUTLIER) cc_final: 0.3888 (mtp180)
REVERT: C  619 ARG cc_start: 0.5399 (OUTLIER) cc_final: 0.3892 (mtp180)
  outliers start: 34
  outliers final: 26
  residues processed: 154
  average time/residue: 0.1340
  time to fit residues: 32.4156
Evaluate side-chains
  147 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 117
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  619 ARG
Chi-restraints excluded: chain A residue  676 TRP
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  619 ARG
Chi-restraints excluded: chain B residue  676 TRP
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  434 LEU
Chi-restraints excluded: chain D residue  461 LEU
Chi-restraints excluded: chain D residue  477 LEU
Chi-restraints excluded: chain D residue  619 ARG
Chi-restraints excluded: chain D residue  676 TRP
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  434 LEU
Chi-restraints excluded: chain C residue  461 LEU
Chi-restraints excluded: chain C residue  477 LEU
Chi-restraints excluded: chain C residue  619 ARG
Chi-restraints excluded: chain C residue  676 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 15 optimal weight:    0.0000
   chunk 116 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 47 optimal weight:    9.9990
   chunk 189 optimal weight:    4.9990
   chunk 98 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 166 optimal weight:    8.9990
   chunk 39 optimal weight:    6.9990
   chunk 96 optimal weight:    5.9990
   chunk 153 optimal weight:    0.9980
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.105871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.098232 restraints weight = 79161.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.099504 restraints weight = 53407.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.100392 restraints weight = 39161.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.100953 restraints weight = 30745.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.101489 restraints weight = 25620.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.4035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.5098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  17656  Z= 0.130
  Angle     :  0.748  19.539  24012  Z= 0.368
  Chirality :  0.042   0.201   2764
  Planarity :  0.004   0.042   2984
  Dihedral  :  5.828  30.298   2392
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.11 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 17.99 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.56 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.18), residues: 2196
  helix:  0.46 (0.14), residues: 1284
  sheet:  None (None), residues: 0
  loop : -1.81 (0.21), residues: 912

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 392 
 TYR   0.029   0.001   TYR C 525 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.007   0.001   TRP C 677 
 HIS   0.003   0.001   HIS A 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (17656)
  covalent geometry    : angle       0.74813 (24012)
  hydrogen bonds       : bond        0.03715 (  897)
  hydrogen bonds       : angle       4.46701 ( 2655)

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

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

  4392 Ramachandran restraints generated.
    2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4392 Ramachandran restraints generated.
    2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 130
  time to evaluate  : 0.720 
Fit side-chains
REVERT: A  372 MET cc_start: 0.7396 (mpp) cc_final: 0.7150 (mpp)
REVERT: A  433 MET cc_start: 0.6076 (ttm) cc_final: 0.5694 (ttp)
REVERT: A  619 ARG cc_start: 0.5560 (OUTLIER) cc_final: 0.3990 (mtp180)
REVERT: A  640 MET cc_start: 0.7641 (tpt) cc_final: 0.7233 (tpt)
REVERT: B  372 MET cc_start: 0.7391 (mpp) cc_final: 0.7142 (mpp)
REVERT: B  619 ARG cc_start: 0.5482 (OUTLIER) cc_final: 0.3882 (mtp180)
REVERT: D  372 MET cc_start: 0.7382 (mpp) cc_final: 0.7127 (mpp)
REVERT: D  619 ARG cc_start: 0.5490 (OUTLIER) cc_final: 0.3882 (mtp180)
REVERT: C  372 MET cc_start: 0.7381 (mpp) cc_final: 0.7136 (mpp)
REVERT: C  619 ARG cc_start: 0.5507 (OUTLIER) cc_final: 0.3891 (mtp180)
  outliers start: 32
  outliers final: 24
  residues processed: 154
  average time/residue: 0.1310
  time to fit residues: 31.9372
Evaluate side-chains
  148 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 120
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  619 ARG
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  619 ARG
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  434 LEU
Chi-restraints excluded: chain D residue  461 LEU
Chi-restraints excluded: chain D residue  477 LEU
Chi-restraints excluded: chain D residue  619 ARG
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  434 LEU
Chi-restraints excluded: chain C residue  461 LEU
Chi-restraints excluded: chain C residue  477 LEU
Chi-restraints excluded: chain C residue  619 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 217 optimal weight:    0.0770
   chunk 74 optimal weight:    6.9990
   chunk 204 optimal weight:    0.8980
   chunk 219 optimal weight:    9.9990
   chunk 0 optimal weight:   50.0000
   chunk 198 optimal weight:    0.8980
   chunk 31 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9980
   chunk 117 optimal weight:    0.0970
   chunk 45 optimal weight:    0.9980
   chunk 97 optimal weight:    5.9990
   overall best weight:    0.5936

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

Flipped N/Q/H residues before XYZ refinement:
** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.109511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.102176 restraints weight = 78426.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.103419 restraints weight = 52091.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.104279 restraints weight = 38136.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.104985 restraints weight = 29804.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.105419 restraints weight = 24124.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.4064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7109
moved from start:          0.5423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051  17656  Z= 0.119
  Angle     :  0.757  20.869  24012  Z= 0.363
  Chirality :  0.042   0.228   2764
  Planarity :  0.004   0.045   2984
  Dihedral  :  5.590  29.361   2392
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 19.14 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.56 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.18), residues: 2196
  helix:  0.64 (0.15), residues: 1288
  sheet:  None (None), residues: 0
  loop : -1.73 (0.21), residues: 908

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 392 
 TYR   0.029   0.001   TYR D 525 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.010   0.001   TRP B 223 
 HIS   0.008   0.001   HIS B 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (17656)
  covalent geometry    : angle       0.75669 (24012)
  hydrogen bonds       : bond        0.03702 (  897)
  hydrogen bonds       : angle       4.37288 ( 2655)

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

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

  4392 Ramachandran restraints generated.
    2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4392 Ramachandran restraints generated.
    2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 156
  time to evaluate  : 0.754 
Fit side-chains
REVERT: A  433 MET cc_start: 0.6192 (ttm) cc_final: 0.5828 (ttp)
REVERT: A  619 ARG cc_start: 0.5381 (OUTLIER) cc_final: 0.4040 (mtp180)
REVERT: A  640 MET cc_start: 0.7376 (tpt) cc_final: 0.7158 (tpt)
REVERT: B  261 PRO cc_start: 0.5682 (Cg_exo) cc_final: 0.5467 (Cg_endo)
REVERT: B  619 ARG cc_start: 0.5161 (OUTLIER) cc_final: 0.3898 (mtp180)
REVERT: D  261 PRO cc_start: 0.5632 (Cg_exo) cc_final: 0.5424 (Cg_endo)
REVERT: D  619 ARG cc_start: 0.5021 (OUTLIER) cc_final: 0.3869 (mtp180)
REVERT: C  261 PRO cc_start: 0.5656 (Cg_exo) cc_final: 0.5447 (Cg_endo)
REVERT: C  524 ILE cc_start: 0.6081 (mp) cc_final: 0.5824 (pt)
REVERT: C  619 ARG cc_start: 0.5018 (OUTLIER) cc_final: 0.3865 (mtp180)
  outliers start: 26
  outliers final: 21
  residues processed: 170
  average time/residue: 0.1526
  time to fit residues: 38.7982
Evaluate side-chains
  168 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  619 ARG
Chi-restraints excluded: chain A residue  676 TRP
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  619 ARG
Chi-restraints excluded: chain B residue  676 TRP
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  434 LEU
Chi-restraints excluded: chain D residue  461 LEU
Chi-restraints excluded: chain D residue  619 ARG
Chi-restraints excluded: chain D residue  676 TRP
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  434 LEU
Chi-restraints excluded: chain C residue  461 LEU
Chi-restraints excluded: chain C residue  619 ARG
Chi-restraints excluded: chain C residue  676 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 146 optimal weight:    9.9990
   chunk 104 optimal weight:    8.9990
   chunk 68 optimal weight:    0.5980
   chunk 66 optimal weight:    7.9990
   chunk 7 optimal weight:    8.9990
   chunk 181 optimal weight:    3.9990
   chunk 78 optimal weight:   10.0000
   chunk 188 optimal weight:    5.9990
   chunk 192 optimal weight:    4.9990
   chunk 136 optimal weight:    0.5980
   chunk 156 optimal weight:    5.9990
   overall best weight:    3.2386

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

Flipped N/Q/H residues before XYZ refinement:
** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.104903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.097828 restraints weight = 79646.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.099053 restraints weight = 52244.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.100001 restraints weight = 37662.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.100564 restraints weight = 28926.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.101098 restraints weight = 23779.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.5277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  17656  Z= 0.151
  Angle     :  0.784  18.353  24012  Z= 0.383
  Chirality :  0.043   0.235   2764
  Planarity :  0.005   0.043   2984
  Dihedral  :  5.864  30.284   2392
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 18.74 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.56 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.18), residues: 2196
  helix:  0.43 (0.14), residues: 1288
  sheet:  None (None), residues: 0
  loop : -1.70 (0.22), residues: 908

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 459 
 TYR   0.032   0.002   TYR D 525 
 PHE   0.015   0.001   PHE B 199 
 TRP   0.008   0.001   TRP B 677 
 HIS   0.006   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (17656)
  covalent geometry    : angle       0.78388 (24012)
  hydrogen bonds       : bond        0.03950 (  897)
  hydrogen bonds       : angle       4.55099 ( 2655)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2517.08 seconds
wall clock time: 44 minutes 34.06 seconds (2674.06 seconds total)