Starting phenix.real_space_refine
on Wed Mar  4 11:11:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n6r_24209/03_2026/7n6r_24209.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n6r_24209/03_2026/7n6r_24209.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n6r_24209/03_2026/7n6r_24209.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n6r_24209/03_2026/7n6r_24209.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n6r_24209/03_2026/7n6r_24209.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n6r_24209/03_2026/7n6r_24209.map"
  }
  resolution = 3.93
  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=   0.005 sd=   1.015
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     100      5.16       5
     C    8656      2.51       5
     N    2004      2.21       5
     O    1948      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12708
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3070
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 3070
          Classifications: {'peptide': 375}
          Link IDs: {'PTRANS': 15, 'TRANS': 359}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 3070
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 3070
          Classifications: {'peptide': 375}
          Link IDs: {'PTRANS': 15, 'TRANS': 359}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 3070
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 3070
          Classifications: {'peptide': 375}
          Link IDs: {'PTRANS': 15, 'TRANS': 359}
          Chain breaks: 4
    Chain: "D"
      Number of atoms: 3070
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 3070
          Classifications: {'peptide': 375}
          Link IDs: {'PTRANS': 15, 'TRANS': 359}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 107
          Unusual residues: {'CLR': 2, 'OLA': 1, 'ROV': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 107
          Unusual residues: {'CLR': 2, 'OLA': 1, 'ROV': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "C"
      Number of atoms: 107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 107
          Unusual residues: {'CLR': 2, 'OLA': 1, 'ROV': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "D"
      Number of atoms: 107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 107
          Unusual residues: {'CLR': 2, 'OLA': 1, 'ROV': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 3.01, per 1000 atoms: 0.24
  Number of scatterers: 12708
  At special positions: 0
  Unit cell: (112.455, 184.093, 74.97, 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     100     16.00
     O    1948      8.00
     N    2004      7.00
     C    8656      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Conformation dependent library (CDL) restraints added in 533.5 milliseconds
  

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2848

  Finding SS restraints...
    Secondary structure from input PDB file:
      80 helices and 0 sheets defined
      80.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 109 through 115
    Processing helix  chain 'A' and resid 117 through 143
      removed outlier: 3.647A  pdb=" N   ARG A 121 " --> pdb=" O   VAL A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 160
    Processing helix  chain 'A' and resid 162 through 189
      Proline residue:  A 172  - end of helix
      Proline residue:  A 181  - end of helix
    Processing helix  chain 'A' and resid 199 through 211
      removed outlier: 3.805A  pdb=" N   ALA A 205 " --> pdb=" O   CYS A 201 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU A 211 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 221
    Processing helix  chain 'A' and resid 226 through 255
      removed outlier: 4.340A  pdb=" N   LEU A 232 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      Proline residue:  A 252  - end of helix
      removed outlier: 3.587A  pdb=" N   LEU A 255 " --> pdb=" O   VAL A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 277
      removed outlier: 3.597A  pdb=" N   PHE A 276 " --> pdb=" O   LEU A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 318
    Processing helix  chain 'A' and resid 319 through 324
      removed outlier: 3.631A  pdb=" N   PHE A 323 " --> pdb=" O   CYS A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 343
      removed outlier: 3.745A  pdb=" N   LEU A 338 " --> pdb=" O   ARG A 334 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   SER A 339 " --> pdb=" O   ALA A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 360
    Processing helix  chain 'A' and resid 361 through 370
    Processing helix  chain 'A' and resid 386 through 394
    Processing helix  chain 'A' and resid 395 through 406
    Processing helix  chain 'A' and resid 406 through 415
      removed outlier: 3.890A  pdb=" N   ARG A 412 " --> pdb=" O   GLN A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 423
      removed outlier: 4.468A  pdb=" N   ALA A 422 " --> pdb=" O   ALA A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 442
      removed outlier: 3.634A  pdb=" N   HIS A 434 " --> pdb=" O   SER A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 462
      removed outlier: 3.837A  pdb=" N   PHE A 462 " --> pdb=" O   GLY A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 499
      removed outlier: 4.171A  pdb=" N   MET A 477 " --> pdb=" O   TRP A 473 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   GLN A 488 " --> pdb=" O   GLY A 484 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   SER A 490 " --> pdb=" O   GLY A 486 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   GLU A 495 " --> pdb=" O   LEU A 491 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   TYR A 497 " --> pdb=" O   CYS A 493 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 115
    Processing helix  chain 'B' and resid 117 through 144
      removed outlier: 3.638A  pdb=" N   ARG B 121 " --> pdb=" O   VAL B 117 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   ILE B 144 " --> pdb=" O   ALA B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 160
    Processing helix  chain 'B' and resid 162 through 189
      Proline residue:  B 172  - end of helix
      Proline residue:  B 181  - end of helix
    Processing helix  chain 'B' and resid 199 through 211
      removed outlier: 3.821A  pdb=" N   ALA B 205 " --> pdb=" O   CYS B 201 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LEU B 211 " --> pdb=" O   HIS B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 221
    Processing helix  chain 'B' and resid 225 through 255
      removed outlier: 4.039A  pdb=" N   LEU B 232 " --> pdb=" O   SER B 228 " (cutoff:3.500A)
      Proline residue:  B 252  - end of helix
      removed outlier: 3.591A  pdb=" N   LEU B 255 " --> pdb=" O   VAL B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 275
    Processing helix  chain 'B' and resid 293 through 318
    Processing helix  chain 'B' and resid 319 through 324
      removed outlier: 3.583A  pdb=" N   PHE B 323 " --> pdb=" O   CYS B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 333 through 343
      removed outlier: 3.727A  pdb=" N   LEU B 338 " --> pdb=" O   ARG B 334 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   SER B 339 " --> pdb=" O   ALA B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 343 through 360
    Processing helix  chain 'B' and resid 361 through 370
    Processing helix  chain 'B' and resid 386 through 394
    Processing helix  chain 'B' and resid 395 through 406
    Processing helix  chain 'B' and resid 406 through 415
      removed outlier: 3.893A  pdb=" N   ARG B 412 " --> pdb=" O   GLN B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 423
      removed outlier: 4.456A  pdb=" N   ALA B 422 " --> pdb=" O   ALA B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 424 through 442
      removed outlier: 3.581A  pdb=" N   HIS B 434 " --> pdb=" O   SER B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 462
      removed outlier: 3.814A  pdb=" N   PHE B 462 " --> pdb=" O   GLY B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 499
      removed outlier: 4.176A  pdb=" N   MET B 477 " --> pdb=" O   TRP B 473 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   GLN B 488 " --> pdb=" O   GLY B 484 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   SER B 490 " --> pdb=" O   GLY B 486 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   GLU B 495 " --> pdb=" O   LEU B 491 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   TYR B 497 " --> pdb=" O   CYS B 493 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 109 through 115
    Processing helix  chain 'C' and resid 117 through 143
      removed outlier: 3.652A  pdb=" N   ARG C 121 " --> pdb=" O   VAL C 117 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 153 through 160
    Processing helix  chain 'C' and resid 162 through 189
      Proline residue:  C 172  - end of helix
      Proline residue:  C 181  - end of helix
    Processing helix  chain 'C' and resid 199 through 211
      removed outlier: 3.803A  pdb=" N   ALA C 205 " --> pdb=" O   CYS C 201 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU C 211 " --> pdb=" O   HIS C 207 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 221
    Processing helix  chain 'C' and resid 226 through 255
      removed outlier: 4.319A  pdb=" N   LEU C 232 " --> pdb=" O   SER C 228 " (cutoff:3.500A)
      Proline residue:  C 252  - end of helix
      removed outlier: 3.587A  pdb=" N   LEU C 255 " --> pdb=" O   VAL C 251 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 267 through 277
      removed outlier: 3.604A  pdb=" N   PHE C 276 " --> pdb=" O   LEU C 272 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 293 through 318
    Processing helix  chain 'C' and resid 319 through 324
      removed outlier: 3.632A  pdb=" N   PHE C 323 " --> pdb=" O   CYS C 319 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 333 through 343
      removed outlier: 3.751A  pdb=" N   LEU C 338 " --> pdb=" O   ARG C 334 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   SER C 339 " --> pdb=" O   ALA C 335 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 343 through 360
    Processing helix  chain 'C' and resid 361 through 370
    Processing helix  chain 'C' and resid 386 through 394
    Processing helix  chain 'C' and resid 395 through 406
    Processing helix  chain 'C' and resid 406 through 415
      removed outlier: 3.904A  pdb=" N   ARG C 412 " --> pdb=" O   GLN C 408 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 418 through 423
      removed outlier: 4.469A  pdb=" N   ALA C 422 " --> pdb=" O   ALA C 418 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 424 through 442
      removed outlier: 3.627A  pdb=" N   HIS C 434 " --> pdb=" O   SER C 430 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 448 through 462
      removed outlier: 3.834A  pdb=" N   PHE C 462 " --> pdb=" O   GLY C 458 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 473 through 499
      removed outlier: 4.170A  pdb=" N   MET C 477 " --> pdb=" O   TRP C 473 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   GLN C 488 " --> pdb=" O   GLY C 484 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   SER C 490 " --> pdb=" O   GLY C 486 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   GLU C 495 " --> pdb=" O   LEU C 491 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   TYR C 497 " --> pdb=" O   CYS C 493 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 109 through 115
    Processing helix  chain 'D' and resid 117 through 144
      removed outlier: 3.637A  pdb=" N   ARG D 121 " --> pdb=" O   VAL D 117 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ILE D 144 " --> pdb=" O   ALA D 140 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 153 through 160
    Processing helix  chain 'D' and resid 162 through 189
      Proline residue:  D 172  - end of helix
      Proline residue:  D 181  - end of helix
    Processing helix  chain 'D' and resid 199 through 211
      removed outlier: 3.824A  pdb=" N   ALA D 205 " --> pdb=" O   CYS D 201 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LEU D 211 " --> pdb=" O   HIS D 207 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 213 through 221
    Processing helix  chain 'D' and resid 225 through 255
      removed outlier: 4.040A  pdb=" N   LEU D 232 " --> pdb=" O   SER D 228 " (cutoff:3.500A)
      Proline residue:  D 252  - end of helix
      removed outlier: 3.591A  pdb=" N   LEU D 255 " --> pdb=" O   VAL D 251 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 267 through 275
    Processing helix  chain 'D' and resid 293 through 318
    Processing helix  chain 'D' and resid 319 through 324
      removed outlier: 3.583A  pdb=" N   PHE D 323 " --> pdb=" O   CYS D 319 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 333 through 343
      removed outlier: 3.729A  pdb=" N   LEU D 338 " --> pdb=" O   ARG D 334 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   SER D 339 " --> pdb=" O   ALA D 335 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 343 through 360
    Processing helix  chain 'D' and resid 361 through 370
    Processing helix  chain 'D' and resid 386 through 394
    Processing helix  chain 'D' and resid 395 through 406
    Processing helix  chain 'D' and resid 406 through 415
      removed outlier: 3.895A  pdb=" N   ARG D 412 " --> pdb=" O   GLN D 408 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 418 through 423
      removed outlier: 4.455A  pdb=" N   ALA D 422 " --> pdb=" O   ALA D 418 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 424 through 442
      removed outlier: 3.579A  pdb=" N   HIS D 434 " --> pdb=" O   SER D 430 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 448 through 462
      removed outlier: 3.814A  pdb=" N   PHE D 462 " --> pdb=" O   GLY D 458 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 473 through 499
      removed outlier: 4.175A  pdb=" N   MET D 477 " --> pdb=" O   TRP D 473 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   GLN D 488 " --> pdb=" O   GLY D 484 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   SER D 490 " --> pdb=" O   GLY D 486 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   GLU D 495 " --> pdb=" O   LEU D 491 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   TYR D 497 " --> pdb=" O   CYS D 493 " (cutoff:3.500A)

    780 hydrogen bonds defined for protein.
    2340 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.85

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1976
        1.33 -     1.45: 3818
        1.45 -     1.57: 7154
        1.57 -     1.69: 16
        1.69 -     1.82: 156
  Bond restraints: 13120
  Sorted by residual:
  bond pdb=" C19 ROV D 601 "
       pdb=" C20 ROV D 601 "
    ideal  model  delta    sigma   weight residual
    1.534  1.367  0.167 2.00e-02 2.50e+03 6.95e+01
  bond pdb=" C19 ROV A 601 "
       pdb=" C20 ROV A 601 "
    ideal  model  delta    sigma   weight residual
    1.534  1.367  0.167 2.00e-02 2.50e+03 6.94e+01
  bond pdb=" C19 ROV B 601 "
       pdb=" C20 ROV B 601 "
    ideal  model  delta    sigma   weight residual
    1.534  1.368  0.166 2.00e-02 2.50e+03 6.90e+01
  bond pdb=" C19 ROV C 601 "
       pdb=" C20 ROV C 601 "
    ideal  model  delta    sigma   weight residual
    1.534  1.368  0.166 2.00e-02 2.50e+03 6.89e+01
  bond pdb=" C18 ROV C 601 "
       pdb=" C22 ROV C 601 "
    ideal  model  delta    sigma   weight residual
    1.538  1.374  0.164 2.00e-02 2.50e+03 6.69e+01
  ... (remaining 13115 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 11279
        1.54 -     3.08: 4970
        3.08 -     4.62: 1367
        4.62 -     6.16: 225
        6.16 -     7.70: 23
  Bond angle restraints: 17864
  Sorted by residual:
  angle pdb=" C   GLY D 457 "
        pdb=" N   GLY D 458 "
        pdb=" CA  GLY D 458 "
      ideal   model   delta    sigma   weight residual
     120.03  125.62   -5.59 1.12e+00 7.97e-01 2.49e+01
  angle pdb=" C   GLY B 457 "
        pdb=" N   GLY B 458 "
        pdb=" CA  GLY B 458 "
      ideal   model   delta    sigma   weight residual
     120.03  125.60   -5.57 1.12e+00 7.97e-01 2.47e+01
  angle pdb=" C   GLY A 457 "
        pdb=" N   GLY A 458 "
        pdb=" CA  GLY A 458 "
      ideal   model   delta    sigma   weight residual
     120.03  125.60   -5.57 1.12e+00 7.97e-01 2.47e+01
  angle pdb=" C   GLY C 457 "
        pdb=" N   GLY C 458 "
        pdb=" CA  GLY C 458 "
      ideal   model   delta    sigma   weight residual
     120.03  125.59   -5.56 1.12e+00 7.97e-01 2.46e+01
  angle pdb=" C   LEU A 199 "
        pdb=" N   GLY A 200 "
        pdb=" CA  GLY A 200 "
      ideal   model   delta    sigma   weight residual
     120.03  125.12   -5.09 1.12e+00 7.97e-01 2.07e+01
  ... (remaining 17859 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 6961
       17.71 -    35.41: 693
       35.41 -    53.12: 170
       53.12 -    70.83: 34
       70.83 -    88.53: 18
  Dihedral angle restraints: 7876
    sinusoidal: 3468
      harmonic: 4408
  Sorted by residual:
  dihedral pdb=" CA  VAL D 117 "
           pdb=" C   VAL D 117 "
           pdb=" N   GLN D 118 "
           pdb=" CA  GLN D 118 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.28  -23.72     0      5.00e+00 4.00e-02 2.25e+01
  dihedral pdb=" CA  VAL C 117 "
           pdb=" C   VAL C 117 "
           pdb=" N   GLN C 118 "
           pdb=" CA  GLN C 118 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.32  -23.68     0      5.00e+00 4.00e-02 2.24e+01
  dihedral pdb=" CA  VAL B 117 "
           pdb=" C   VAL B 117 "
           pdb=" N   GLN B 118 "
           pdb=" CA  GLN B 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.52  -23.48     0      5.00e+00 4.00e-02 2.21e+01
  ... (remaining 7873 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1009
       0.058 -    0.116: 715
       0.116 -    0.173: 233
       0.173 -    0.231: 15
       0.231 -    0.289: 12
  Chirality restraints: 1984
  Sorted by residual:
  chirality pdb=" C13 CLR A 603 "
            pdb=" C12 CLR A 603 "
            pdb=" C14 CLR A 603 "
            pdb=" C17 CLR A 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.64   -0.29 2.00e-01 2.50e+01 2.08e+00
  chirality pdb=" C13 CLR D 602 "
            pdb=" C12 CLR D 602 "
            pdb=" C14 CLR D 602 "
            pdb=" C17 CLR D 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.65   -0.29 2.00e-01 2.50e+01 2.05e+00
  chirality pdb=" C13 CLR B 603 "
            pdb=" C12 CLR B 603 "
            pdb=" C14 CLR B 603 "
            pdb=" C17 CLR B 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.65   -0.28 2.00e-01 2.50e+01 2.02e+00
  ... (remaining 1981 not shown)

  Planarity restraints: 2108
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 490 "    0.010 2.00e-02 2.50e+03   2.01e-02 4.06e+00
        pdb=" C   SER A 490 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   SER A 490 "    0.013 2.00e-02 2.50e+03
        pdb=" N   LEU A 491 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C 490 "   -0.010 2.00e-02 2.50e+03   2.01e-02 4.05e+00
        pdb=" C   SER C 490 "    0.035 2.00e-02 2.50e+03
        pdb=" O   SER C 490 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LEU C 491 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 490 "   -0.009 2.00e-02 2.50e+03   1.95e-02 3.81e+00
        pdb=" C   SER B 490 "    0.034 2.00e-02 2.50e+03
        pdb=" O   SER B 490 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LEU B 491 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 2105 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1339
        2.79 -     3.32: 13402
        3.32 -     3.85: 19526
        3.85 -     4.37: 24118
        4.37 -     4.90: 40058
  Nonbonded interactions: 98443
  Sorted by model distance:
  nonbonded pdb=" O   ILE C 281 "
            pdb=" OH  TYR C 286 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   ILE A 281 "
            pdb=" OH  TYR A 286 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   ILE D 281 "
            pdb=" OH  TYR D 286 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" O   ILE B 281 "
            pdb=" OH  TYR B 286 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" NE2 GLN D 236 "
            pdb=" OH  TYR D 436 "
     model   vdw
     2.395 3.120
  ... (remaining 98438 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             2.300
  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:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.910
  Find NCS groups from input model:        0.220
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
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      :  0.015   0.167  13120  Z= 1.093
  Angle     :  1.794   7.702  17864  Z= 1.333
  Chirality :  0.078   0.289   1984
  Planarity :  0.004   0.020   2108
  Dihedral  : 15.717  88.533   5028
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.14 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  8.20 %
    Favored  : 90.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.93 (0.18), residues: 1460
  helix: -2.25 (0.13), residues: 1044
  sheet:  None (None), residues: 0
  loop : -3.07 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 392 
 TYR   0.020   0.003   TYR A 271 
 PHE   0.028   0.003   PHE C 444 
 TRP   0.019   0.002   TRP C 401 
 HIS   0.008   0.002   HIS C 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.01517 (13120)
  covalent geometry    : angle       1.79362 (17864)
  hydrogen bonds       : bond        0.17050 (  780)
  hydrogen bonds       : angle       8.96107 ( 2340)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  409 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 393
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 GLN cc_start: 0.8215 (mt0) cc_final: 0.7946 (mp10)
REVERT: A  122 THR cc_start: 0.8837 (m) cc_final: 0.8574 (m)
REVERT: A  135 ILE cc_start: 0.7723 (tt) cc_final: 0.7488 (tt)
REVERT: A  284 GLU cc_start: 0.8456 (pp20) cc_final: 0.7832 (pt0)
REVERT: A  374 ASP cc_start: 0.7715 (t0) cc_final: 0.7342 (t0)
REVERT: A  442 LEU cc_start: 0.8203 (mt) cc_final: 0.7987 (mt)
REVERT: A  444 PHE cc_start: 0.6957 (m-80) cc_final: 0.6523 (m-80)
REVERT: A  480 MET cc_start: 0.7851 (mmt) cc_final: 0.7094 (tmm)
REVERT: B  169 THR cc_start: 0.8313 (t) cc_final: 0.8077 (p)
REVERT: B  170 TRP cc_start: 0.8127 (t60) cc_final: 0.7350 (t60)
REVERT: B  247 LEU cc_start: 0.9193 (mm) cc_final: 0.8805 (tt)
REVERT: B  274 PHE cc_start: 0.8400 (t80) cc_final: 0.8134 (t80)
REVERT: B  350 MET cc_start: 0.7928 (mmm) cc_final: 0.6976 (tmm)
REVERT: B  360 HIS cc_start: 0.8052 (t70) cc_final: 0.7311 (t70)
REVERT: B  380 ASP cc_start: 0.7305 (p0) cc_final: 0.6611 (p0)
REVERT: B  381 TRP cc_start: 0.9071 (p-90) cc_final: 0.8842 (p-90)
REVERT: B  393 THR cc_start: 0.8673 (p) cc_final: 0.7810 (t)
REVERT: B  419 ARG cc_start: 0.5983 (ptt-90) cc_final: 0.4807 (ptm160)
REVERT: B  423 MET cc_start: 0.8165 (ttp) cc_final: 0.7944 (tpp)
REVERT: B  435 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7531 (mm-30)
REVERT: B  473 TRP cc_start: 0.7827 (t-100) cc_final: 0.6694 (m-90)
REVERT: C  115 MET cc_start: 0.8317 (tpt) cc_final: 0.8111 (tpt)
REVERT: C  374 ASP cc_start: 0.7769 (t0) cc_final: 0.7198 (t0)
REVERT: C  444 PHE cc_start: 0.7026 (m-80) cc_final: 0.6510 (m-80)
REVERT: D  102 LYS cc_start: 0.7984 (tttm) cc_final: 0.7476 (tppt)
REVERT: D  170 TRP cc_start: 0.8076 (t60) cc_final: 0.7051 (t60)
REVERT: D  247 LEU cc_start: 0.9139 (mm) cc_final: 0.8730 (tt)
REVERT: D  266 PRO cc_start: 0.7397 (Cg_endo) cc_final: 0.6564 (Cg_exo)
REVERT: D  379 ARG cc_start: 0.7511 (mtm180) cc_final: 0.7043 (mtp85)
REVERT: D  380 ASP cc_start: 0.6825 (p0) cc_final: 0.6510 (p0)
REVERT: D  391 TYR cc_start: 0.7876 (m-80) cc_final: 0.7487 (t80)
REVERT: D  393 THR cc_start: 0.8475 (p) cc_final: 0.7616 (t)
REVERT: D  428 LEU cc_start: 0.8825 (tp) cc_final: 0.8594 (pp)
REVERT: D  435 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7458 (mm-30)
REVERT: D  473 TRP cc_start: 0.7937 (t-100) cc_final: 0.6625 (m-90)
REVERT: D  476 LEU cc_start: 0.8259 (tt) cc_final: 0.7426 (mm)
  outliers start: 16
  outliers final: 3
  residues processed: 401
  average time/residue: 0.1094
  time to fit residues: 63.3177
Evaluate side-chains
  273 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 268
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain B residue  435 GLU
Chi-restraints excluded: chain C residue  435 GLU
Chi-restraints excluded: chain D residue  435 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    0.0870
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 207 HIS
A 236 GLN
B 207 HIS
B 217 HIS
B 236 GLN
** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 162 GLN
C 207 HIS
C 236 GLN
D 217 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.150735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.122941 restraints weight = 22284.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.125671 restraints weight = 13055.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.127333 restraints weight = 9226.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.128566 restraints weight = 7427.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.128906 restraints weight = 6486.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13120  Z= 0.149
  Angle     :  0.723   9.949  17864  Z= 0.346
  Chirality :  0.041   0.145   1984
  Planarity :  0.005   0.040   2108
  Dihedral  :  9.326  86.708   2330
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 19.58 %
    Favored  : 76.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.22), residues: 1460
  helix: -0.06 (0.15), residues: 1060
  sheet:  None (None), residues: 0
  loop : -2.43 (0.33), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 317 
 TYR   0.021   0.001   TYR D 391 
 PHE   0.015   0.001   PHE B 143 
 TRP   0.027   0.001   TRP D 188 
 HIS   0.004   0.001   HIS A 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (13120)
  covalent geometry    : angle       0.72330 (17864)
  hydrogen bonds       : bond        0.04107 (  780)
  hydrogen bonds       : angle       5.16272 ( 2340)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  376 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 326
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 ILE cc_start: 0.8475 (tt) cc_final: 0.8232 (tt)
REVERT: A  338 LEU cc_start: 0.7985 (tp) cc_final: 0.7768 (tp)
REVERT: A  368 GLU cc_start: 0.8183 (tp30) cc_final: 0.7744 (tp30)
REVERT: A  442 LEU cc_start: 0.8629 (mt) cc_final: 0.8384 (mt)
REVERT: A  444 PHE cc_start: 0.8273 (m-80) cc_final: 0.7669 (m-80)
REVERT: B  247 LEU cc_start: 0.8673 (mm) cc_final: 0.8194 (tt)
REVERT: B  281 ILE cc_start: 0.8686 (mm) cc_final: 0.8308 (tp)
REVERT: B  300 ASN cc_start: 0.7630 (m-40) cc_final: 0.7110 (t0)
REVERT: B  350 MET cc_start: 0.7790 (mmm) cc_final: 0.7448 (mpp)
REVERT: B  366 PHE cc_start: 0.8921 (m-80) cc_final: 0.8661 (m-10)
REVERT: B  380 ASP cc_start: 0.7074 (p0) cc_final: 0.6818 (p0)
REVERT: B  393 THR cc_start: 0.8924 (p) cc_final: 0.8528 (t)
REVERT: B  419 ARG cc_start: 0.5860 (ptt-90) cc_final: 0.4770 (ptm160)
REVERT: B  473 TRP cc_start: 0.7641 (t-100) cc_final: 0.6996 (m-90)
REVERT: C  188 TRP cc_start: 0.6411 (t-100) cc_final: 0.6144 (t-100)
REVERT: C  223 GLN cc_start: 0.6606 (mt0) cc_final: 0.6331 (pp30)
REVERT: C  368 GLU cc_start: 0.8145 (tp30) cc_final: 0.7863 (tp30)
REVERT: C  391 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.6843 (t80)
REVERT: C  444 PHE cc_start: 0.8364 (m-80) cc_final: 0.7543 (m-80)
REVERT: D  170 TRP cc_start: 0.8166 (t60) cc_final: 0.7580 (t60)
REVERT: D  201 CYS cc_start: 0.6938 (m) cc_final: 0.6183 (p)
REVERT: D  237 VAL cc_start: 0.8858 (m) cc_final: 0.8650 (p)
REVERT: D  247 LEU cc_start: 0.8567 (mm) cc_final: 0.8124 (tt)
REVERT: D  380 ASP cc_start: 0.6438 (p0) cc_final: 0.6028 (p0)
REVERT: D  473 TRP cc_start: 0.7704 (t-100) cc_final: 0.7088 (m-90)
REVERT: D  476 LEU cc_start: 0.8792 (tt) cc_final: 0.7763 (mm)
  outliers start: 50
  outliers final: 23
  residues processed: 352
  average time/residue: 0.0929
  time to fit residues: 49.6699
Evaluate side-chains
  296 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 272
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  456 ILE
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain C residue  354 ILE
Chi-restraints excluded: chain C residue  391 TYR
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  138 THR
Chi-restraints excluded: chain D residue  211 LEU
Chi-restraints excluded: chain D residue  228 SER
Chi-restraints excluded: chain D residue  251 VAL
Chi-restraints excluded: chain D residue  281 ILE
Chi-restraints excluded: chain D residue  411 LEU
Chi-restraints excluded: chain D residue  426 VAL
Chi-restraints excluded: chain D residue  451 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 146 optimal weight:    4.9990
   chunk 85 optimal weight:    0.2980
   chunk 109 optimal weight:    0.8980
   chunk 116 optimal weight:    5.9990
   chunk 87 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 123 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 110 optimal weight:    1.9990
   chunk 141 optimal weight:    9.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
A 119 HIS
** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 HIS
C 119 HIS
D 119 HIS
D 217 HIS
D 236 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.146028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.117899 restraints weight = 22670.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.120344 restraints weight = 13818.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.121960 restraints weight = 10054.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.122810 restraints weight = 8227.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.122990 restraints weight = 7319.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.3946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  13120  Z= 0.193
  Angle     :  0.753  10.316  17864  Z= 0.358
  Chirality :  0.045   0.244   1984
  Planarity :  0.005   0.042   2108
  Dihedral  :  8.191  59.318   2316
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 23.68 %
    Favored  : 71.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.22), residues: 1460
  helix:  0.49 (0.15), residues: 1076
  sheet:  None (None), residues: 0
  loop : -2.43 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 379 
 TYR   0.016   0.002   TYR B 182 
 PHE   0.016   0.002   PHE C 453 
 TRP   0.018   0.001   TRP C 478 
 HIS   0.008   0.001   HIS D 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 (13120)
  covalent geometry    : angle       0.75298 (17864)
  hydrogen bonds       : bond        0.04131 (  780)
  hydrogen bonds       : angle       4.90520 ( 2340)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  368 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 304
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 ILE cc_start: 0.8670 (tt) cc_final: 0.8461 (tt)
REVERT: A  223 GLN cc_start: 0.6523 (mt0) cc_final: 0.6280 (pp30)
REVERT: A  368 GLU cc_start: 0.8324 (tp30) cc_final: 0.8028 (tp30)
REVERT: A  442 LEU cc_start: 0.8658 (mt) cc_final: 0.8414 (mt)
REVERT: A  444 PHE cc_start: 0.8514 (m-80) cc_final: 0.7923 (m-80)
REVERT: B  170 TRP cc_start: 0.8109 (t60) cc_final: 0.7706 (t60)
REVERT: B  224 LEU cc_start: 0.8359 (mm) cc_final: 0.8105 (mm)
REVERT: B  247 LEU cc_start: 0.8715 (mm) cc_final: 0.8125 (tt)
REVERT: B  281 ILE cc_start: 0.8878 (mm) cc_final: 0.8620 (mm)
REVERT: B  300 ASN cc_start: 0.7658 (m-40) cc_final: 0.7165 (t0)
REVERT: B  350 MET cc_start: 0.7736 (mmm) cc_final: 0.7404 (tpp)
REVERT: B  419 ARG cc_start: 0.5687 (ptt-90) cc_final: 0.4207 (ptm160)
REVERT: B  473 TRP cc_start: 0.7732 (t-100) cc_final: 0.7099 (m-90)
REVERT: B  492 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.7619 (m-80)
REVERT: C  368 GLU cc_start: 0.8283 (tp30) cc_final: 0.7955 (tp30)
REVERT: C  391 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.7194 (t80)
REVERT: C  444 PHE cc_start: 0.8396 (m-80) cc_final: 0.7527 (m-80)
REVERT: D  170 TRP cc_start: 0.8132 (t60) cc_final: 0.6900 (t60)
REVERT: D  224 LEU cc_start: 0.8249 (mm) cc_final: 0.7881 (mm)
REVERT: D  237 VAL cc_start: 0.8925 (m) cc_final: 0.8691 (p)
REVERT: D  247 LEU cc_start: 0.8617 (mm) cc_final: 0.8091 (tt)
REVERT: D  380 ASP cc_start: 0.7119 (p0) cc_final: 0.6703 (p0)
REVERT: D  473 TRP cc_start: 0.7711 (t-100) cc_final: 0.7086 (m-90)
REVERT: D  476 LEU cc_start: 0.8824 (tt) cc_final: 0.7733 (mm)
REVERT: D  492 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.7927 (m-80)
  outliers start: 64
  outliers final: 41
  residues processed: 340
  average time/residue: 0.0847
  time to fit residues: 45.0676
Evaluate side-chains
  313 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 269
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  349 PHE
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  384 SER
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  143 PHE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  312 CYS
Chi-restraints excluded: chain B residue  354 ILE
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  456 ILE
Chi-restraints excluded: chain B residue  492 TYR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  344 THR
Chi-restraints excluded: chain C residue  349 PHE
Chi-restraints excluded: chain C residue  354 ILE
Chi-restraints excluded: chain C residue  384 SER
Chi-restraints excluded: chain C residue  391 TYR
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  211 LEU
Chi-restraints excluded: chain D residue  228 SER
Chi-restraints excluded: chain D residue  251 VAL
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  308 VAL
Chi-restraints excluded: chain D residue  354 ILE
Chi-restraints excluded: chain D residue  411 LEU
Chi-restraints excluded: chain D residue  426 VAL
Chi-restraints excluded: chain D residue  451 ILE
Chi-restraints excluded: chain D residue  475 VAL
Chi-restraints excluded: chain D residue  492 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 116 optimal weight:    2.9990
   chunk 90 optimal weight:    0.1980
   chunk 97 optimal weight:    1.9990
   chunk 127 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 71 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9980
   chunk 92 optimal weight:    0.5980
   chunk 139 optimal weight:    5.9990
   chunk 107 optimal weight:    0.8980
   chunk 132 optimal weight:    9.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 119 HIS
C 383 ASN
D 217 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.148619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.120840 restraints weight = 22566.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.123447 restraints weight = 13322.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.125158 restraints weight = 9447.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.126082 restraints weight = 7630.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.126475 restraints weight = 6727.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.4377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13120  Z= 0.134
  Angle     :  0.680  10.270  17864  Z= 0.319
  Chirality :  0.041   0.194   1984
  Planarity :  0.005   0.045   2108
  Dihedral  :  7.715  58.173   2316
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 26.01 %
    Favored  : 69.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.22), residues: 1460
  helix:  0.79 (0.16), residues: 1108
  sheet:  None (None), residues: 0
  loop : -2.33 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 379 
 TYR   0.018   0.001   TYR B 182 
 PHE   0.011   0.001   PHE A 120 
 TRP   0.013   0.001   TRP C 478 
 HIS   0.006   0.001   HIS D 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (13120)
  covalent geometry    : angle       0.67986 (17864)
  hydrogen bonds       : bond        0.03527 (  780)
  hydrogen bonds       : angle       4.62737 ( 2340)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  349 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 293
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 ILE cc_start: 0.8570 (tt) cc_final: 0.8322 (tt)
REVERT: A  187 LEU cc_start: 0.8660 (pp) cc_final: 0.8453 (mt)
REVERT: A  188 TRP cc_start: 0.6899 (m-10) cc_final: 0.6651 (m-10)
REVERT: A  223 GLN cc_start: 0.6571 (mt0) cc_final: 0.6240 (pp30)
REVERT: A  368 GLU cc_start: 0.8283 (tp30) cc_final: 0.7891 (tp30)
REVERT: A  444 PHE cc_start: 0.8504 (m-80) cc_final: 0.7939 (m-80)
REVERT: B  142 ASP cc_start: 0.7616 (t0) cc_final: 0.7401 (t0)
REVERT: B  224 LEU cc_start: 0.8263 (mm) cc_final: 0.8013 (mm)
REVERT: B  235 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7486 (tp30)
REVERT: B  281 ILE cc_start: 0.8843 (mm) cc_final: 0.8538 (mm)
REVERT: B  300 ASN cc_start: 0.7384 (m-40) cc_final: 0.6917 (t0)
REVERT: B  350 MET cc_start: 0.7743 (mmm) cc_final: 0.7403 (tpp)
REVERT: B  419 ARG cc_start: 0.5583 (ptt-90) cc_final: 0.4227 (ptm160)
REVERT: B  473 TRP cc_start: 0.7748 (t-100) cc_final: 0.7055 (m-90)
REVERT: B  492 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.7575 (m-80)
REVERT: C  341 LEU cc_start: 0.8494 (tp) cc_final: 0.8117 (tp)
REVERT: C  368 GLU cc_start: 0.8292 (tp30) cc_final: 0.7874 (tp30)
REVERT: C  391 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.6868 (t80)
REVERT: C  444 PHE cc_start: 0.8222 (m-10) cc_final: 0.7701 (m-10)
REVERT: D  224 LEU cc_start: 0.8325 (mm) cc_final: 0.8029 (mm)
REVERT: D  237 VAL cc_start: 0.8955 (m) cc_final: 0.8751 (p)
REVERT: D  300 ASN cc_start: 0.6905 (t0) cc_final: 0.6656 (t0)
REVERT: D  326 MET cc_start: 0.5882 (tmm) cc_final: 0.5531 (ppp)
REVERT: D  380 ASP cc_start: 0.7170 (p0) cc_final: 0.6827 (p0)
REVERT: D  473 TRP cc_start: 0.7802 (t-100) cc_final: 0.7161 (m-90)
REVERT: D  480 MET cc_start: 0.8087 (mmt) cc_final: 0.7708 (mmm)
REVERT: D  492 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.7838 (m-80)
REVERT: D  497 TYR cc_start: 0.7508 (m-10) cc_final: 0.7286 (m-10)
  outliers start: 56
  outliers final: 41
  residues processed: 322
  average time/residue: 0.0866
  time to fit residues: 43.6654
Evaluate side-chains
  315 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 271
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  349 PHE
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  312 CYS
Chi-restraints excluded: chain B residue  354 ILE
Chi-restraints excluded: chain B residue  391 TYR
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  456 ILE
Chi-restraints excluded: chain B residue  492 TYR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  115 MET
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain C residue  247 LEU
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  349 PHE
Chi-restraints excluded: chain C residue  354 ILE
Chi-restraints excluded: chain C residue  391 TYR
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  138 THR
Chi-restraints excluded: chain D residue  141 ILE
Chi-restraints excluded: chain D residue  211 LEU
Chi-restraints excluded: chain D residue  228 SER
Chi-restraints excluded: chain D residue  251 VAL
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  289 THR
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  354 ILE
Chi-restraints excluded: chain D residue  411 LEU
Chi-restraints excluded: chain D residue  426 VAL
Chi-restraints excluded: chain D residue  451 ILE
Chi-restraints excluded: chain D residue  492 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 71 optimal weight:    7.9990
   chunk 11 optimal weight:    0.9990
   chunk 126 optimal weight:    0.8980
   chunk 134 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 57 optimal weight:    6.9990
   chunk 123 optimal weight:    0.7980
   chunk 52 optimal weight:    6.9990
   chunk 39 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 383 ASN
B 119 HIS
B 217 HIS
C 119 HIS
C 222 HIS
D 125 HIS
D 217 HIS
D 236 GLN
D 408 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.148797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.120500 restraints weight = 22552.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.123178 restraints weight = 13004.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.124946 restraints weight = 9125.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.125936 restraints weight = 7316.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.126671 restraints weight = 6421.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.4796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13120  Z= 0.134
  Angle     :  0.688  10.329  17864  Z= 0.319
  Chirality :  0.041   0.177   1984
  Planarity :  0.004   0.044   2108
  Dihedral  :  7.048  59.988   2316
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 25.70 %
    Favored  : 69.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.22), residues: 1460
  helix:  0.99 (0.16), residues: 1088
  sheet:  None (None), residues: 0
  loop : -2.38 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 379 
 TYR   0.018   0.001   TYR B 182 
 PHE   0.014   0.001   PHE C 120 
 TRP   0.010   0.001   TRP C 478 
 HIS   0.005   0.001   HIS C 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (13120)
  covalent geometry    : angle       0.68764 (17864)
  hydrogen bonds       : bond        0.03453 (  780)
  hydrogen bonds       : angle       4.52882 ( 2340)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  353 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 286
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 ILE cc_start: 0.8613 (tt) cc_final: 0.8396 (tt)
REVERT: A  188 TRP cc_start: 0.6966 (m-10) cc_final: 0.6746 (m-10)
REVERT: A  223 GLN cc_start: 0.6651 (mt0) cc_final: 0.6295 (pp30)
REVERT: A  328 ARG cc_start: 0.7944 (tmm-80) cc_final: 0.6872 (tpm170)
REVERT: A  368 GLU cc_start: 0.8249 (tp30) cc_final: 0.7914 (tp30)
REVERT: A  444 PHE cc_start: 0.8555 (m-80) cc_final: 0.8043 (m-80)
REVERT: A  459 MET cc_start: 0.6033 (ttm) cc_final: 0.5698 (tpt)
REVERT: B  142 ASP cc_start: 0.7749 (t0) cc_final: 0.7493 (t0)
REVERT: B  224 LEU cc_start: 0.8243 (mm) cc_final: 0.8009 (mm)
REVERT: B  235 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7632 (tp30)
REVERT: B  281 ILE cc_start: 0.8846 (mm) cc_final: 0.8468 (mm)
REVERT: B  300 ASN cc_start: 0.7378 (m-40) cc_final: 0.6894 (t0)
REVERT: B  419 ARG cc_start: 0.5626 (ptt-90) cc_final: 0.4182 (ptm160)
REVERT: B  453 PHE cc_start: 0.7769 (t80) cc_final: 0.7536 (t80)
REVERT: B  473 TRP cc_start: 0.7727 (t-100) cc_final: 0.7063 (m-90)
REVERT: B  492 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.7672 (m-80)
REVERT: C  286 TYR cc_start: 0.8263 (m-80) cc_final: 0.8062 (m-80)
REVERT: C  341 LEU cc_start: 0.8581 (tp) cc_final: 0.8141 (tp)
REVERT: C  368 GLU cc_start: 0.8294 (tp30) cc_final: 0.7930 (tp30)
REVERT: C  444 PHE cc_start: 0.8130 (m-10) cc_final: 0.7842 (m-10)
REVERT: C  459 MET cc_start: 0.5301 (ttm) cc_final: 0.4784 (ttt)
REVERT: D  224 LEU cc_start: 0.8328 (mm) cc_final: 0.8067 (mm)
REVERT: D  237 VAL cc_start: 0.8966 (m) cc_final: 0.8761 (p)
REVERT: D  300 ASN cc_start: 0.7101 (t0) cc_final: 0.6729 (t0)
REVERT: D  326 MET cc_start: 0.6139 (tmm) cc_final: 0.5623 (ppp)
REVERT: D  449 MET cc_start: 0.6185 (tmm) cc_final: 0.4782 (tpt)
REVERT: D  473 TRP cc_start: 0.7855 (t-100) cc_final: 0.7227 (m-90)
REVERT: D  492 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7923 (m-80)
REVERT: D  497 TYR cc_start: 0.7582 (m-10) cc_final: 0.7358 (m-10)
  outliers start: 67
  outliers final: 48
  residues processed: 324
  average time/residue: 0.0856
  time to fit residues: 43.5592
Evaluate side-chains
  322 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 272
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  349 PHE
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  312 CYS
Chi-restraints excluded: chain B residue  354 ILE
Chi-restraints excluded: chain B residue  391 TYR
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  456 ILE
Chi-restraints excluded: chain B residue  492 TYR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  105 ILE
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain C residue  173 MET
Chi-restraints excluded: chain C residue  210 VAL
Chi-restraints excluded: chain C residue  247 LEU
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  295 ASN
Chi-restraints excluded: chain C residue  349 PHE
Chi-restraints excluded: chain C residue  354 ILE
Chi-restraints excluded: chain C residue  391 TYR
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  138 THR
Chi-restraints excluded: chain D residue  141 ILE
Chi-restraints excluded: chain D residue  211 LEU
Chi-restraints excluded: chain D residue  228 SER
Chi-restraints excluded: chain D residue  251 VAL
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  308 VAL
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  354 ILE
Chi-restraints excluded: chain D residue  411 LEU
Chi-restraints excluded: chain D residue  426 VAL
Chi-restraints excluded: chain D residue  451 ILE
Chi-restraints excluded: chain D residue  492 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 102 optimal weight:    0.7980
   chunk 83 optimal weight:    0.7980
   chunk 128 optimal weight:    5.9990
   chunk 103 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 139 optimal weight:    0.9990
   chunk 129 optimal weight:    1.9990
   chunk 4 optimal weight:    7.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 383 ASN
B 217 HIS
** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 217 HIS
** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.148900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.120821 restraints weight = 22253.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.123435 restraints weight = 12724.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.125220 restraints weight = 8856.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.126296 restraints weight = 7070.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.126836 restraints weight = 6188.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.5069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13120  Z= 0.133
  Angle     :  0.695  11.207  17864  Z= 0.320
  Chirality :  0.041   0.221   1984
  Planarity :  0.004   0.044   2108
  Dihedral  :  6.882  58.352   2316
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 27.48 %
    Favored  : 67.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.23), residues: 1460
  helix:  1.10 (0.16), residues: 1088
  sheet:  None (None), residues: 0
  loop : -2.40 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 238 
 TYR   0.017   0.001   TYR D 182 
 PHE   0.011   0.001   PHE C 120 
 TRP   0.012   0.001   TRP A 478 
 HIS   0.004   0.001   HIS C 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (13120)
  covalent geometry    : angle       0.69463 (17864)
  hydrogen bonds       : bond        0.03388 (  780)
  hydrogen bonds       : angle       4.46528 ( 2340)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 292
  time to evaluate  : 0.483 
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: A  135 ILE cc_start: 0.8590 (tt) cc_final: 0.8382 (tt)
REVERT: A  368 GLU cc_start: 0.8249 (tp30) cc_final: 0.7892 (tp30)
REVERT: A  444 PHE cc_start: 0.8575 (m-80) cc_final: 0.7691 (m-80)
REVERT: B  224 LEU cc_start: 0.8170 (mm) cc_final: 0.7945 (mm)
REVERT: B  235 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7577 (tp30)
REVERT: B  281 ILE cc_start: 0.8826 (mm) cc_final: 0.8400 (tp)
REVERT: B  300 ASN cc_start: 0.7415 (m-40) cc_final: 0.6929 (t0)
REVERT: B  408 GLN cc_start: 0.7913 (mt0) cc_final: 0.7508 (mm-40)
REVERT: B  419 ARG cc_start: 0.5520 (ptt-90) cc_final: 0.4033 (ptm160)
REVERT: B  428 LEU cc_start: 0.9144 (tp) cc_final: 0.8767 (pp)
REVERT: B  473 TRP cc_start: 0.7743 (t-100) cc_final: 0.7083 (m-90)
REVERT: C  341 LEU cc_start: 0.8534 (tp) cc_final: 0.8102 (tp)
REVERT: C  368 GLU cc_start: 0.8276 (tp30) cc_final: 0.7999 (tp30)
REVERT: C  444 PHE cc_start: 0.8135 (m-10) cc_final: 0.7921 (m-10)
REVERT: D  173 MET cc_start: 0.9022 (ppp) cc_final: 0.8768 (ppp)
REVERT: D  224 LEU cc_start: 0.8250 (mm) cc_final: 0.8010 (mm)
REVERT: D  300 ASN cc_start: 0.7129 (t0) cc_final: 0.6737 (t0)
REVERT: D  326 MET cc_start: 0.6108 (tmm) cc_final: 0.5672 (ppp)
REVERT: D  419 ARG cc_start: 0.4964 (ptt-90) cc_final: 0.4181 (ptm160)
REVERT: D  449 MET cc_start: 0.5726 (tmm) cc_final: 0.5064 (tpt)
REVERT: D  473 TRP cc_start: 0.7845 (t-100) cc_final: 0.7120 (m-90)
REVERT: D  497 TYR cc_start: 0.7674 (m-10) cc_final: 0.7426 (m-10)
  outliers start: 63
  outliers final: 52
  residues processed: 328
  average time/residue: 0.0866
  time to fit residues: 44.2680
Evaluate side-chains
  327 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 275
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  115 MET
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  349 PHE
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  384 SER
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  312 CYS
Chi-restraints excluded: chain B residue  354 ILE
Chi-restraints excluded: chain B residue  391 TYR
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  456 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  105 ILE
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain C residue  173 MET
Chi-restraints excluded: chain C residue  175 LEU
Chi-restraints excluded: chain C residue  210 VAL
Chi-restraints excluded: chain C residue  247 LEU
Chi-restraints excluded: chain C residue  295 ASN
Chi-restraints excluded: chain C residue  349 PHE
Chi-restraints excluded: chain C residue  354 ILE
Chi-restraints excluded: chain C residue  391 TYR
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  134 PHE
Chi-restraints excluded: chain D residue  138 THR
Chi-restraints excluded: chain D residue  141 ILE
Chi-restraints excluded: chain D residue  211 LEU
Chi-restraints excluded: chain D residue  228 SER
Chi-restraints excluded: chain D residue  251 VAL
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  289 THR
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  354 ILE
Chi-restraints excluded: chain D residue  411 LEU
Chi-restraints excluded: chain D residue  426 VAL
Chi-restraints excluded: chain D residue  451 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 110 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 120 optimal weight:   20.0000
   chunk 26 optimal weight:    1.9990
   chunk 95 optimal weight:    0.0980
   chunk 112 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 82 optimal weight:    3.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
B 217 HIS
** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 488 GLN
D 217 HIS
** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.160495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.134814 restraints weight = 22269.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.137410 restraints weight = 12700.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.139115 restraints weight = 8834.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.140049 restraints weight = 7022.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.140529 restraints weight = 6148.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.5289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  13120  Z= 0.128
  Angle     :  0.699  10.868  17864  Z= 0.321
  Chirality :  0.040   0.146   1984
  Planarity :  0.004   0.043   2108
  Dihedral  :  6.618  55.937   2316
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 27.79 %
    Favored  : 67.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.22), residues: 1460
  helix:  1.10 (0.16), residues: 1100
  sheet:  None (None), residues: 0
  loop : -2.74 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 379 
 TYR   0.018   0.001   TYR D 182 
 PHE   0.015   0.001   PHE A 387 
 TRP   0.014   0.001   TRP C 478 
 HIS   0.004   0.001   HIS D 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (13120)
  covalent geometry    : angle       0.69860 (17864)
  hydrogen bonds       : bond        0.03342 (  780)
  hydrogen bonds       : angle       4.39005 ( 2340)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  348 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 285
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  368 GLU cc_start: 0.8214 (tp30) cc_final: 0.7848 (tp30)
REVERT: A  444 PHE cc_start: 0.8652 (m-80) cc_final: 0.8143 (m-80)
REVERT: B  142 ASP cc_start: 0.7619 (t0) cc_final: 0.7365 (t0)
REVERT: B  173 MET cc_start: 0.8899 (ppp) cc_final: 0.8682 (ppp)
REVERT: B  235 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7319 (tp30)
REVERT: B  281 ILE cc_start: 0.8776 (mm) cc_final: 0.8411 (mm)
REVERT: B  300 ASN cc_start: 0.7307 (m-40) cc_final: 0.6937 (t0)
REVERT: B  428 LEU cc_start: 0.9167 (tp) cc_final: 0.8845 (pp)
REVERT: B  473 TRP cc_start: 0.7638 (t-100) cc_final: 0.7044 (m-90)
REVERT: C  368 GLU cc_start: 0.8220 (tp30) cc_final: 0.7911 (tp30)
REVERT: C  444 PHE cc_start: 0.8135 (m-10) cc_final: 0.7753 (m-10)
REVERT: D  224 LEU cc_start: 0.8200 (mm) cc_final: 0.7979 (mm)
REVERT: D  300 ASN cc_start: 0.7101 (t0) cc_final: 0.6775 (t0)
REVERT: D  326 MET cc_start: 0.6203 (tmm) cc_final: 0.5856 (ppp)
REVERT: D  449 MET cc_start: 0.5679 (tmm) cc_final: 0.5219 (tpt)
REVERT: D  473 TRP cc_start: 0.7798 (t-100) cc_final: 0.7189 (m-90)
  outliers start: 63
  outliers final: 51
  residues processed: 316
  average time/residue: 0.0861
  time to fit residues: 42.5925
Evaluate side-chains
  326 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 275
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  115 MET
Chi-restraints excluded: chain A residue  134 PHE
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  349 PHE
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain B residue  134 PHE
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  312 CYS
Chi-restraints excluded: chain B residue  349 PHE
Chi-restraints excluded: chain B residue  354 ILE
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  456 ILE
Chi-restraints excluded: chain C residue  105 ILE
Chi-restraints excluded: chain C residue  113 GLU
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain C residue  173 MET
Chi-restraints excluded: chain C residue  175 LEU
Chi-restraints excluded: chain C residue  210 VAL
Chi-restraints excluded: chain C residue  247 LEU
Chi-restraints excluded: chain C residue  295 ASN
Chi-restraints excluded: chain C residue  349 PHE
Chi-restraints excluded: chain C residue  354 ILE
Chi-restraints excluded: chain C residue  391 TYR
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  134 PHE
Chi-restraints excluded: chain D residue  138 THR
Chi-restraints excluded: chain D residue  141 ILE
Chi-restraints excluded: chain D residue  211 LEU
Chi-restraints excluded: chain D residue  228 SER
Chi-restraints excluded: chain D residue  251 VAL
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  289 THR
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  354 ILE
Chi-restraints excluded: chain D residue  411 LEU
Chi-restraints excluded: chain D residue  426 VAL
Chi-restraints excluded: chain D residue  451 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 144 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 121 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   chunk 10 optimal weight:    0.3980
   chunk 122 optimal weight:    7.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
B 217 HIS
** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 434 HIS
D 217 HIS
** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.146845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.118457 restraints weight = 22304.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.121049 restraints weight = 12859.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.122762 restraints weight = 9059.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.123703 restraints weight = 7288.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 55)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.124457 restraints weight = 6428.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.5384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  13120  Z= 0.162
  Angle     :  0.727  11.674  17864  Z= 0.337
  Chirality :  0.042   0.156   1984
  Planarity :  0.004   0.043   2108
  Dihedral  :  6.617  57.858   2316
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 27.63 %
    Favored  : 67.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.22), residues: 1460
  helix:  1.08 (0.16), residues: 1100
  sheet:  None (None), residues: 0
  loop : -2.81 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 375 
 TYR   0.016   0.001   TYR B 182 
 PHE   0.012   0.001   PHE B 387 
 TRP   0.016   0.001   TRP A 478 
 HIS   0.006   0.001   HIS C 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (13120)
  covalent geometry    : angle       0.72731 (17864)
  hydrogen bonds       : bond        0.03550 (  780)
  hydrogen bonds       : angle       4.45852 ( 2340)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  345 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 280
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  368 GLU cc_start: 0.8386 (tp30) cc_final: 0.8090 (tp30)
REVERT: A  444 PHE cc_start: 0.8687 (m-80) cc_final: 0.8209 (m-80)
REVERT: B  142 ASP cc_start: 0.7630 (t0) cc_final: 0.7426 (t0)
REVERT: B  235 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7394 (tp30)
REVERT: B  281 ILE cc_start: 0.8900 (mm) cc_final: 0.8568 (mm)
REVERT: B  300 ASN cc_start: 0.7493 (m-40) cc_final: 0.7040 (t0)
REVERT: B  408 GLN cc_start: 0.7848 (mt0) cc_final: 0.7633 (mm-40)
REVERT: B  428 LEU cc_start: 0.9143 (tp) cc_final: 0.8834 (pp)
REVERT: B  473 TRP cc_start: 0.7687 (t-100) cc_final: 0.7123 (m-90)
REVERT: B  492 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7570 (m-80)
REVERT: C  368 GLU cc_start: 0.8348 (tp30) cc_final: 0.8050 (tp30)
REVERT: C  444 PHE cc_start: 0.8191 (m-10) cc_final: 0.7862 (m-10)
REVERT: D  142 ASP cc_start: 0.7520 (t0) cc_final: 0.7278 (t0)
REVERT: D  224 LEU cc_start: 0.8258 (mm) cc_final: 0.8017 (mm)
REVERT: D  300 ASN cc_start: 0.7342 (t0) cc_final: 0.6916 (t0)
REVERT: D  326 MET cc_start: 0.6301 (tmm) cc_final: 0.5933 (ppp)
REVERT: D  449 MET cc_start: 0.5681 (tmm) cc_final: 0.5170 (tpt)
REVERT: D  473 TRP cc_start: 0.7706 (t-100) cc_final: 0.7111 (m-90)
REVERT: D  497 TYR cc_start: 0.7770 (m-10) cc_final: 0.7509 (m-10)
  outliers start: 65
  outliers final: 53
  residues processed: 318
  average time/residue: 0.0826
  time to fit residues: 41.4295
Evaluate side-chains
  316 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 262
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  349 PHE
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  217 HIS
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  312 CYS
Chi-restraints excluded: chain B residue  349 PHE
Chi-restraints excluded: chain B residue  354 ILE
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  456 ILE
Chi-restraints excluded: chain B residue  492 TYR
Chi-restraints excluded: chain C residue  105 ILE
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain C residue  175 LEU
Chi-restraints excluded: chain C residue  210 VAL
Chi-restraints excluded: chain C residue  295 ASN
Chi-restraints excluded: chain C residue  349 PHE
Chi-restraints excluded: chain C residue  354 ILE
Chi-restraints excluded: chain C residue  384 SER
Chi-restraints excluded: chain C residue  391 TYR
Chi-restraints excluded: chain C residue  438 PHE
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  134 PHE
Chi-restraints excluded: chain D residue  138 THR
Chi-restraints excluded: chain D residue  141 ILE
Chi-restraints excluded: chain D residue  211 LEU
Chi-restraints excluded: chain D residue  228 SER
Chi-restraints excluded: chain D residue  251 VAL
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  289 THR
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  354 ILE
Chi-restraints excluded: chain D residue  391 TYR
Chi-restraints excluded: chain D residue  411 LEU
Chi-restraints excluded: chain D residue  426 VAL
Chi-restraints excluded: chain D residue  451 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 114 optimal weight:    4.9990
   chunk 37 optimal weight:    6.9990
   chunk 81 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 119 optimal weight:    0.3980
   chunk 77 optimal weight:    0.6980
   chunk 75 optimal weight:    0.0870
   chunk 45 optimal weight:    0.2980
   chunk 52 optimal weight:    3.9990
   chunk 139 optimal weight:    0.8980
   chunk 137 optimal weight:    1.9990
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
B 217 HIS
B 434 HIS
C 399 HIS
D 217 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.162427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.137015 restraints weight = 22271.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.139664 restraints weight = 12706.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.141382 restraints weight = 8764.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.142253 restraints weight = 6945.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.143034 restraints weight = 6096.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.5667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  13120  Z= 0.126
  Angle     :  0.721  11.835  17864  Z= 0.333
  Chirality :  0.040   0.203   1984
  Planarity :  0.004   0.042   2108
  Dihedral  :  6.468  58.962   2316
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 29.64 %
    Favored  : 66.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.22), residues: 1460
  helix:  1.17 (0.16), residues: 1096
  sheet:  None (None), residues: 0
  loop : -2.67 (0.29), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 375 
 TYR   0.040   0.001   TYR A 436 
 PHE   0.011   0.001   PHE B 453 
 TRP   0.018   0.001   TRP A 478 
 HIS   0.005   0.001   HIS B 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (13120)
  covalent geometry    : angle       0.72133 (17864)
  hydrogen bonds       : bond        0.03372 (  780)
  hydrogen bonds       : angle       4.35244 ( 2340)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 281
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  368 GLU cc_start: 0.8360 (tp30) cc_final: 0.7947 (tp30)
REVERT: A  374 ASP cc_start: 0.8260 (t70) cc_final: 0.7771 (t0)
REVERT: A  444 PHE cc_start: 0.8621 (m-80) cc_final: 0.8312 (m-80)
REVERT: B  142 ASP cc_start: 0.7532 (t0) cc_final: 0.7327 (t0)
REVERT: B  173 MET cc_start: 0.8813 (ppp) cc_final: 0.8588 (ppp)
REVERT: B  300 ASN cc_start: 0.7250 (m-40) cc_final: 0.6938 (t0)
REVERT: B  428 LEU cc_start: 0.9139 (tp) cc_final: 0.8931 (pp)
REVERT: C  341 LEU cc_start: 0.8494 (tp) cc_final: 0.8112 (tp)
REVERT: C  368 GLU cc_start: 0.8294 (tp30) cc_final: 0.7907 (tp30)
REVERT: C  374 ASP cc_start: 0.8463 (t70) cc_final: 0.7907 (t0)
REVERT: C  444 PHE cc_start: 0.8105 (m-10) cc_final: 0.7439 (m-10)
REVERT: C  449 MET cc_start: 0.7397 (tpp) cc_final: 0.6713 (tpt)
REVERT: D  142 ASP cc_start: 0.7387 (t0) cc_final: 0.7172 (t0)
REVERT: D  224 LEU cc_start: 0.8134 (mm) cc_final: 0.7929 (mm)
REVERT: D  300 ASN cc_start: 0.6902 (t0) cc_final: 0.6613 (t0)
REVERT: D  391 TYR cc_start: 0.6403 (OUTLIER) cc_final: 0.5922 (m-80)
REVERT: D  423 MET cc_start: 0.8311 (tpt) cc_final: 0.7224 (tpp)
REVERT: D  449 MET cc_start: 0.5664 (tmm) cc_final: 0.5207 (tpt)
REVERT: D  473 TRP cc_start: 0.7671 (t-100) cc_final: 0.7142 (m-90)
REVERT: D  495 GLU cc_start: 0.5431 (OUTLIER) cc_final: 0.4904 (mp0)
  outliers start: 51
  outliers final: 42
  residues processed: 308
  average time/residue: 0.0814
  time to fit residues: 40.0222
Evaluate side-chains
  303 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 259
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  115 MET
Chi-restraints excluded: chain A residue  126 MET
Chi-restraints excluded: chain A residue  134 PHE
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  349 PHE
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain B residue  134 PHE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  217 HIS
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  312 CYS
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  456 ILE
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain C residue  175 LEU
Chi-restraints excluded: chain C residue  210 VAL
Chi-restraints excluded: chain C residue  247 LEU
Chi-restraints excluded: chain C residue  295 ASN
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain C residue  349 PHE
Chi-restraints excluded: chain C residue  354 ILE
Chi-restraints excluded: chain C residue  391 TYR
Chi-restraints excluded: chain C residue  438 PHE
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  134 PHE
Chi-restraints excluded: chain D residue  141 ILE
Chi-restraints excluded: chain D residue  211 LEU
Chi-restraints excluded: chain D residue  217 HIS
Chi-restraints excluded: chain D residue  228 SER
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  289 THR
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  391 TYR
Chi-restraints excluded: chain D residue  411 LEU
Chi-restraints excluded: chain D residue  426 VAL
Chi-restraints excluded: chain D residue  451 ILE
Chi-restraints excluded: chain D residue  495 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 90 optimal weight:    0.4980
   chunk 100 optimal weight:    0.6980
   chunk 34 optimal weight:    6.9990
   chunk 134 optimal weight:    2.9990
   chunk 88 optimal weight:    0.4980
   chunk 121 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 102 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 217 HIS
** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 434 HIS
D 217 HIS
** D 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.161342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.135491 restraints weight = 22160.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.138112 restraints weight = 12726.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.139878 restraints weight = 8868.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.140753 restraints weight = 7048.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.141283 restraints weight = 6199.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.5807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  13120  Z= 0.135
  Angle     :  0.742  13.392  17864  Z= 0.343
  Chirality :  0.041   0.260   1984
  Planarity :  0.005   0.042   2108
  Dihedral  :  6.524  59.435   2316
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.21 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 30.42 %
    Favored  : 66.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.22), residues: 1460
  helix:  1.19 (0.16), residues: 1100
  sheet:  None (None), residues: 0
  loop : -2.63 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 375 
 TYR   0.040   0.001   TYR A 436 
 PHE   0.023   0.001   PHE D 239 
 TRP   0.020   0.001   TRP C 478 
 HIS   0.005   0.001   HIS B 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (13120)
  covalent geometry    : angle       0.74193 (17864)
  hydrogen bonds       : bond        0.03448 (  780)
  hydrogen bonds       : angle       4.35582 ( 2340)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 265
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 TYR cc_start: 0.8107 (m-80) cc_final: 0.7753 (t80)
REVERT: A  341 LEU cc_start: 0.8176 (tp) cc_final: 0.7577 (tp)
REVERT: A  368 GLU cc_start: 0.8391 (tp30) cc_final: 0.8001 (tp30)
REVERT: A  374 ASP cc_start: 0.8274 (t70) cc_final: 0.7843 (t0)
REVERT: B  173 MET cc_start: 0.8887 (ppp) cc_final: 0.8682 (ppp)
REVERT: B  281 ILE cc_start: 0.8758 (mm) cc_final: 0.8457 (mm)
REVERT: B  300 ASN cc_start: 0.7269 (m-40) cc_final: 0.6923 (t0)
REVERT: B  376 MET cc_start: 0.7528 (ttp) cc_final: 0.6823 (tmm)
REVERT: C  341 LEU cc_start: 0.8490 (tp) cc_final: 0.8104 (tp)
REVERT: C  368 GLU cc_start: 0.8326 (tp30) cc_final: 0.8019 (tp30)
REVERT: D  142 ASP cc_start: 0.7375 (t0) cc_final: 0.7072 (t0)
REVERT: D  203 LEU cc_start: 0.8494 (mt) cc_final: 0.7882 (tp)
REVERT: D  224 LEU cc_start: 0.8242 (mm) cc_final: 0.8008 (mm)
REVERT: D  300 ASN cc_start: 0.7080 (t0) cc_final: 0.6736 (t0)
REVERT: D  391 TYR cc_start: 0.6326 (OUTLIER) cc_final: 0.5866 (m-80)
REVERT: D  449 MET cc_start: 0.5622 (tmm) cc_final: 0.5178 (tpt)
REVERT: D  473 TRP cc_start: 0.7623 (t-100) cc_final: 0.7101 (m-90)
REVERT: D  495 GLU cc_start: 0.5345 (OUTLIER) cc_final: 0.4762 (mp0)
  outliers start: 43
  outliers final: 33
  residues processed: 288
  average time/residue: 0.0845
  time to fit residues: 38.5891
Evaluate side-chains
  283 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 248
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 PHE
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  349 PHE
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  312 CYS
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain C residue  175 LEU
Chi-restraints excluded: chain C residue  210 VAL
Chi-restraints excluded: chain C residue  295 ASN
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain C residue  349 PHE
Chi-restraints excluded: chain C residue  354 ILE
Chi-restraints excluded: chain C residue  391 TYR
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  134 PHE
Chi-restraints excluded: chain D residue  211 LEU
Chi-restraints excluded: chain D residue  217 HIS
Chi-restraints excluded: chain D residue  228 SER
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  289 THR
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  391 TYR
Chi-restraints excluded: chain D residue  426 VAL
Chi-restraints excluded: chain D residue  439 CYS
Chi-restraints excluded: chain D residue  451 ILE
Chi-restraints excluded: chain D residue  495 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 47 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 77 optimal weight:    0.8980
   chunk 69 optimal weight:    0.4980
   chunk 121 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 31 optimal weight:    0.6980
   chunk 85 optimal weight:    0.3980
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 119 HIS
B 217 HIS
** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 434 HIS
D 217 HIS
D 434 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.161804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.136036 restraints weight = 22067.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.138584 restraints weight = 12612.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.139996 restraints weight = 8733.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.141230 restraints weight = 7067.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.141624 restraints weight = 6109.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.5945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  13120  Z= 0.136
  Angle     :  0.759  12.693  17864  Z= 0.350
  Chirality :  0.041   0.244   1984
  Planarity :  0.005   0.041   2108
  Dihedral  :  6.435  59.180   2316
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.86 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 30.11 %
    Favored  : 65.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.22), residues: 1460
  helix:  1.15 (0.16), residues: 1100
  sheet:  None (None), residues: 0
  loop : -2.58 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 375 
 TYR   0.036   0.001   TYR A 436 
 PHE   0.024   0.001   PHE B 440 
 TRP   0.019   0.001   TRP C 478 
 HIS   0.012   0.001   HIS D 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (13120)
  covalent geometry    : angle       0.75940 (17864)
  hydrogen bonds       : bond        0.03448 (  780)
  hydrogen bonds       : angle       4.32463 ( 2340)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2058.40 seconds
wall clock time: 36 minutes 20.96 seconds (2180.96 seconds total)