Starting phenix.real_space_refine
on Wed Mar  4 06:53:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mkh_23894/03_2026/7mkh_23894.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mkh_23894/03_2026/7mkh_23894.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mkh_23894/03_2026/7mkh_23894.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mkh_23894/03_2026/7mkh_23894.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mkh_23894/03_2026/7mkh_23894.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mkh_23894/03_2026/7mkh_23894.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    3600      2.51       5
     N    1060      2.21       5
     O    1070      1.98       5
     H    5980      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  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: 11720
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "B"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "C"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "D"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "E"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "F"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "G"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "H"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "I"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "J"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
  Time building chain proxies: 2.23, per 1000 atoms: 0.19
  Number of scatterers: 11720
  At special positions: 0
  Unit cell: (137.984, 98.098, 47.432, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     O    1070      8.00
     N    1060      7.00
     C    3600      6.00
     H    5980      1.00
    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: 0.86
  Conformation dependent library (CDL) restraints added in 352.7 milliseconds
  

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1320

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 16 sheets defined
      0.0% alpha, 49.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310
    Processing sheet with id=AA2, first strand: chain 'A' and resid 316 through 320
      removed outlier: 6.513A  pdb=" N   SER A 316 " --> pdb=" O   LYS C 317 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   THR C 319 " --> pdb=" O   SER A 316 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   VAL A 318 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   SER C 316 " --> pdb=" O   LYS E 317 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   THR E 319 " --> pdb=" O   SER C 316 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   VAL C 318 " --> pdb=" O   THR E 319 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   SER E 316 " --> pdb=" O   LYS G 317 " (cutoff:3.500A)
      removed outlier: 7.772A  pdb=" N   THR G 319 " --> pdb=" O   SER E 316 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   VAL E 318 " --> pdb=" O   THR G 319 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   SER G 316 " --> pdb=" O   LYS I 317 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   THR I 319 " --> pdb=" O   SER G 316 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   VAL G 318 " --> pdb=" O   THR I 319 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 329 through 330
    Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 340
      removed outlier: 6.583A  pdb=" N   VAL A 337 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   LYS C 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   VAL A 339 " --> pdb=" O   LYS C 340 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   VAL C 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 8.111A  pdb=" N   LYS E 340 " --> pdb=" O   VAL C 337 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   VAL C 339 " --> pdb=" O   LYS E 340 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   VAL E 337 " --> pdb=" O   GLU G 338 " (cutoff:3.500A)
      removed outlier: 8.111A  pdb=" N   LYS G 340 " --> pdb=" O   VAL E 337 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   VAL E 339 " --> pdb=" O   LYS G 340 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   VAL G 337 " --> pdb=" O   GLU I 338 " (cutoff:3.500A)
      removed outlier: 8.111A  pdb=" N   LYS I 340 " --> pdb=" O   VAL G 337 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   VAL G 339 " --> pdb=" O   LYS I 340 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 347
      removed outlier: 6.386A  pdb=" N   LEU A 344 " --> pdb=" O   ASP C 345 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   LYS C 347 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   PHE A 346 " --> pdb=" O   LYS C 347 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   LEU C 344 " --> pdb=" O   ASP E 345 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   LYS E 347 " --> pdb=" O   LEU C 344 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   PHE C 346 " --> pdb=" O   LYS E 347 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   LEU E 344 " --> pdb=" O   ASP G 345 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   LYS G 347 " --> pdb=" O   LEU E 344 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   PHE E 346 " --> pdb=" O   LYS G 347 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   LEU G 344 " --> pdb=" O   ASP I 345 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   LYS I 347 " --> pdb=" O   LEU G 344 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   PHE G 346 " --> pdb=" O   LYS I 347 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 356
      removed outlier: 6.910A  pdb=" N   SER A 356 " --> pdb=" O   GLY C 355 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   SER C 356 " --> pdb=" O   GLY E 355 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   SER E 356 " --> pdb=" O   GLY G 355 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   SER G 356 " --> pdb=" O   GLY I 355 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 360 through 362
      removed outlier: 6.309A  pdb=" N   THR A 361 " --> pdb=" O   HIS C 362 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   THR C 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   THR E 361 " --> pdb=" O   HIS G 362 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   THR G 361 " --> pdb=" O   HIS I 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 367 through 376
    Processing sheet with id=AA9, first strand: chain 'B' and resid 306 through 310
      removed outlier: 6.343A  pdb=" N   VAL B 306 " --> pdb=" O   GLN D 307 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   VAL D 309 " --> pdb=" O   VAL B 306 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ILE B 308 " --> pdb=" O   VAL D 309 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   VAL D 306 " --> pdb=" O   GLN F 307 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   VAL F 309 " --> pdb=" O   VAL D 306 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ILE D 308 " --> pdb=" O   VAL F 309 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   VAL F 306 " --> pdb=" O   GLN H 307 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   VAL H 309 " --> pdb=" O   VAL F 306 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ILE F 308 " --> pdb=" O   VAL H 309 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   VAL H 306 " --> pdb=" O   GLN J 307 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   VAL J 309 " --> pdb=" O   VAL H 306 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ILE H 308 " --> pdb=" O   VAL J 309 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 316 through 324
      removed outlier: 6.413A  pdb=" N   SER B 316 " --> pdb=" O   LYS D 317 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   THR D 319 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   VAL B 318 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   LYS D 321 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   SER B 320 " --> pdb=" O   LYS D 321 " (cutoff:3.500A)
      removed outlier: 8.454A  pdb=" N   GLY D 323 " --> pdb=" O   SER B 320 " (cutoff:3.500A)
      removed outlier: 8.912A  pdb=" N   CYS B 322 " --> pdb=" O   GLY D 323 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   SER D 316 " --> pdb=" O   LYS F 317 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   THR F 319 " --> pdb=" O   SER D 316 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   VAL D 318 " --> pdb=" O   THR F 319 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   LYS F 321 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   SER D 320 " --> pdb=" O   LYS F 321 " (cutoff:3.500A)
      removed outlier: 8.455A  pdb=" N   GLY F 323 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
      removed outlier: 8.912A  pdb=" N   CYS D 322 " --> pdb=" O   GLY F 323 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   SER F 316 " --> pdb=" O   LYS H 317 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   THR H 319 " --> pdb=" O   SER F 316 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   VAL F 318 " --> pdb=" O   THR H 319 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   LYS H 321 " --> pdb=" O   VAL F 318 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   SER F 320 " --> pdb=" O   LYS H 321 " (cutoff:3.500A)
      removed outlier: 8.454A  pdb=" N   GLY H 323 " --> pdb=" O   SER F 320 " (cutoff:3.500A)
      removed outlier: 8.912A  pdb=" N   CYS F 322 " --> pdb=" O   GLY H 323 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   SER H 316 " --> pdb=" O   LYS J 317 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   THR J 319 " --> pdb=" O   SER H 316 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   VAL H 318 " --> pdb=" O   THR J 319 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   LYS J 321 " --> pdb=" O   VAL H 318 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   SER H 320 " --> pdb=" O   LYS J 321 " (cutoff:3.500A)
      removed outlier: 8.455A  pdb=" N   GLY J 323 " --> pdb=" O   SER H 320 " (cutoff:3.500A)
      removed outlier: 8.912A  pdb=" N   CYS H 322 " --> pdb=" O   GLY J 323 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 329 through 330
    Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 340
      removed outlier: 6.564A  pdb=" N   VAL B 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
      removed outlier: 7.883A  pdb=" N   LYS D 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   VAL B 339 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   VAL D 337 " --> pdb=" O   GLU F 338 " (cutoff:3.500A)
      removed outlier: 7.883A  pdb=" N   LYS F 340 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   VAL D 339 " --> pdb=" O   LYS F 340 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   VAL F 337 " --> pdb=" O   GLU H 338 " (cutoff:3.500A)
      removed outlier: 7.884A  pdb=" N   LYS H 340 " --> pdb=" O   VAL F 337 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   VAL F 339 " --> pdb=" O   LYS H 340 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   VAL H 337 " --> pdb=" O   GLU J 338 " (cutoff:3.500A)
      removed outlier: 7.883A  pdb=" N   LYS J 340 " --> pdb=" O   VAL H 337 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   VAL H 339 " --> pdb=" O   LYS J 340 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'B' and resid 343 through 347
    Processing sheet with id=AB5, first strand: chain 'B' and resid 350 through 356
      removed outlier: 6.901A  pdb=" N   SER B 356 " --> pdb=" O   GLY D 355 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   SER D 356 " --> pdb=" O   GLY F 355 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   SER F 356 " --> pdb=" O   GLY H 355 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   SER H 356 " --> pdb=" O   GLY J 355 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 360 through 362
      removed outlier: 6.309A  pdb=" N   THR B 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   THR D 361 " --> pdb=" O   HIS F 362 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   THR F 361 " --> pdb=" O   HIS H 362 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   THR H 361 " --> pdb=" O   HIS J 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'B' and resid 367 through 378

    160 hydrogen bonds defined for protein.
    480 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.31

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        0.95 -     1.12: 5970
        1.12 -     1.30: 961
        1.30 -     1.47: 2344
        1.47 -     1.64: 2525
        1.64 -     1.82: 10
  Bond restraints: 11810
  Sorted by residual:
  bond pdb=" NE2 HIS G 374 "
       pdb=" HE2 HIS G 374 "
    ideal  model  delta    sigma   weight residual
    0.860  1.049 -0.189 2.00e-02 2.50e+03 8.90e+01
  bond pdb=" NE2 HIS E 374 "
       pdb=" HE2 HIS E 374 "
    ideal  model  delta    sigma   weight residual
    0.860  1.048 -0.188 2.00e-02 2.50e+03 8.85e+01
  bond pdb=" NE2 HIS I 374 "
       pdb=" HE2 HIS I 374 "
    ideal  model  delta    sigma   weight residual
    0.860  1.048 -0.188 2.00e-02 2.50e+03 8.83e+01
  bond pdb=" NE2 HIS A 374 "
       pdb=" HE2 HIS A 374 "
    ideal  model  delta    sigma   weight residual
    0.860  1.048 -0.188 2.00e-02 2.50e+03 8.83e+01
  bond pdb=" NE2 HIS C 374 "
       pdb=" HE2 HIS C 374 "
    ideal  model  delta    sigma   weight residual
    0.860  1.048 -0.188 2.00e-02 2.50e+03 8.81e+01
  ... (remaining 11805 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.06: 18744
        3.06 -     6.11: 1925
        6.11 -     9.16: 741
        9.16 -    12.22: 105
       12.22 -    15.27: 5
  Bond angle restraints: 21520
  Sorted by residual:
  angle pdb=" CA  PHE E 378 "
        pdb=" CB  PHE E 378 "
        pdb=" CG  PHE E 378 "
      ideal   model   delta    sigma   weight residual
     113.80  120.69   -6.89 1.00e+00 1.00e+00 4.75e+01
  angle pdb=" CA  PHE G 378 "
        pdb=" CB  PHE G 378 "
        pdb=" CG  PHE G 378 "
      ideal   model   delta    sigma   weight residual
     113.80  120.69   -6.89 1.00e+00 1.00e+00 4.74e+01
  angle pdb=" CA  PHE C 378 "
        pdb=" CB  PHE C 378 "
        pdb=" CG  PHE C 378 "
      ideal   model   delta    sigma   weight residual
     113.80  120.68   -6.88 1.00e+00 1.00e+00 4.74e+01
  angle pdb=" CA  PHE I 378 "
        pdb=" CB  PHE I 378 "
        pdb=" CG  PHE I 378 "
      ideal   model   delta    sigma   weight residual
     113.80  120.68   -6.88 1.00e+00 1.00e+00 4.74e+01
  angle pdb=" CA  PHE A 378 "
        pdb=" CB  PHE A 378 "
        pdb=" CG  PHE A 378 "
      ideal   model   delta    sigma   weight residual
     113.80  120.68   -6.88 1.00e+00 1.00e+00 4.73e+01
  ... (remaining 21515 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.32: 5040
       13.32 -    26.64: 190
       26.64 -    39.97: 95
       39.97 -    53.29: 70
       53.29 -    66.61: 45
  Dihedral angle restraints: 5440
    sinusoidal: 3110
      harmonic: 2330
  Sorted by residual:
  dihedral pdb=" CD2 HIS F 330 "
           pdb=" CG  HIS F 330 "
           pdb=" ND1 HIS F 330 "
           pdb=" HD1 HIS F 330 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.91   17.09     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CD2 HIS J 330 "
           pdb=" CG  HIS J 330 "
           pdb=" ND1 HIS J 330 "
           pdb=" HD1 HIS J 330 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.95   17.05     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CD2 HIS D 330 "
           pdb=" CG  HIS D 330 "
           pdb=" ND1 HIS D 330 "
           pdb=" HD1 HIS D 330 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.95   17.05     0      5.00e+00 4.00e-02 1.16e+01
  ... (remaining 5437 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 458
       0.068 -    0.135: 284
       0.135 -    0.203: 113
       0.203 -    0.271: 20
       0.271 -    0.338: 5
  Chirality restraints: 880
  Sorted by residual:
  chirality pdb=" CA  PHE D 346 "
            pdb=" N   PHE D 346 "
            pdb=" C   PHE D 346 "
            pdb=" CB  PHE D 346 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.86e+00
  chirality pdb=" CA  PHE F 346 "
            pdb=" N   PHE F 346 "
            pdb=" C   PHE F 346 "
            pdb=" CB  PHE F 346 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.85e+00
  chirality pdb=" CA  PHE J 346 "
            pdb=" N   PHE J 346 "
            pdb=" C   PHE J 346 "
            pdb=" CB  PHE J 346 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.82e+00
  ... (remaining 877 not shown)

  Planarity restraints: 1700
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS J 330 "   -0.049 2.00e-02 2.50e+03   6.21e-02 8.68e+01
        pdb=" CG  HIS J 330 "   -0.048 2.00e-02 2.50e+03
        pdb=" ND1 HIS J 330 "   -0.061 2.00e-02 2.50e+03
        pdb=" CD2 HIS J 330 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 HIS J 330 "   -0.030 2.00e-02 2.50e+03
        pdb=" NE2 HIS J 330 "    0.018 2.00e-02 2.50e+03
        pdb=" HD1 HIS J 330 "    0.143 2.00e-02 2.50e+03
        pdb=" HD2 HIS J 330 "    0.055 2.00e-02 2.50e+03
        pdb=" HE1 HIS J 330 "   -0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS F 330 "   -0.049 2.00e-02 2.50e+03   6.21e-02 8.68e+01
        pdb=" CG  HIS F 330 "   -0.048 2.00e-02 2.50e+03
        pdb=" ND1 HIS F 330 "   -0.061 2.00e-02 2.50e+03
        pdb=" CD2 HIS F 330 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 HIS F 330 "   -0.030 2.00e-02 2.50e+03
        pdb=" NE2 HIS F 330 "    0.018 2.00e-02 2.50e+03
        pdb=" HD1 HIS F 330 "    0.143 2.00e-02 2.50e+03
        pdb=" HD2 HIS F 330 "    0.054 2.00e-02 2.50e+03
        pdb=" HE1 HIS F 330 "   -0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS D 330 "   -0.049 2.00e-02 2.50e+03   6.21e-02 8.66e+01
        pdb=" CG  HIS D 330 "   -0.048 2.00e-02 2.50e+03
        pdb=" ND1 HIS D 330 "   -0.061 2.00e-02 2.50e+03
        pdb=" CD2 HIS D 330 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 HIS D 330 "   -0.029 2.00e-02 2.50e+03
        pdb=" NE2 HIS D 330 "    0.018 2.00e-02 2.50e+03
        pdb=" HD1 HIS D 330 "    0.143 2.00e-02 2.50e+03
        pdb=" HD2 HIS D 330 "    0.055 2.00e-02 2.50e+03
        pdb=" HE1 HIS D 330 "   -0.039 2.00e-02 2.50e+03
  ... (remaining 1697 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.18: 1161
        2.18 -     2.79: 22392
        2.79 -     3.39: 30288
        3.39 -     4.00: 42645
        4.00 -     4.60: 61443
  Nonbonded interactions: 157929
  Sorted by model distance:
  nonbonded pdb=" HD1 HIS D 330 "
            pdb=" OG1 THR D 361 "
     model   vdw
     1.580 2.450
  nonbonded pdb=" HD1 HIS B 330 "
            pdb=" OG1 THR B 361 "
     model   vdw
     1.581 2.450
  nonbonded pdb=" HD1 HIS J 330 "
            pdb=" OG1 THR J 361 "
     model   vdw
     1.581 2.450
  nonbonded pdb=" HD1 HIS H 330 "
            pdb=" OG1 THR H 361 "
     model   vdw
     1.581 2.450
  nonbonded pdb=" HD1 HIS F 330 "
            pdb=" OG1 THR F 361 "
     model   vdw
     1.581 2.450
  ... (remaining 157924 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.070
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.080
  Find NCS groups from input model:        0.140
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6827
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      :  0.023   0.190   5830  Z= 1.254
  Angle     :  1.991   9.386   7800  Z= 1.304
  Chirality :  0.097   0.338    880
  Planarity :  0.009   0.030    990
  Dihedral  :  8.929  66.609   2240
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 0.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  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: -2.24 (0.24), residues: 730
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.70 (0.18), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 349 
 TYR   0.026   0.010   TYR F 310 
 PHE   0.030   0.007   PHE E 378 
 HIS   0.007   0.003   HIS H 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.02259 ( 5830)
  covalent geometry    : angle       1.99092 ( 7800)
  hydrogen bonds       : bond        0.13765 (  160)
  hydrogen bonds       : angle      10.29374 (  480)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.2839
  time to fit residues: 56.9029
Evaluate side-chains
  79 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.088373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.076172 restraints weight = 69867.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.4198 rms_B_bonded: 6.84
r_work: 0.4080 rms_B_bonded: 6.05 restraints_weight: 2.0000
r_work (final): 0.4080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6344
moved from start:          0.4538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   5830  Z= 0.234
  Angle     :  0.752   8.541   7800  Z= 0.410
  Chirality :  0.053   0.157    880
  Planarity :  0.004   0.032    990
  Dihedral  :  5.655  19.248    770
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 10.15 %
    Favored  : 88.94 %
  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: -2.35 (0.24), residues: 730
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.18), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 349 
 TYR   0.007   0.002   TYR B 310 
 PHE   0.016   0.002   PHE D 346 
 HIS   0.005   0.001   HIS C 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 ( 5830)
  covalent geometry    : angle       0.75165 ( 7800)
  hydrogen bonds       : bond        0.06208 (  160)
  hydrogen bonds       : angle       7.19733 (  480)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  348 ASP cc_start: 0.8532 (t0) cc_final: 0.8276 (m-30)
REVERT: B  358 ASP cc_start: 0.8706 (p0) cc_final: 0.8316 (m-30)
REVERT: C  348 ASP cc_start: 0.8031 (t0) cc_final: 0.7752 (m-30)
REVERT: D  378 PHE cc_start: 0.8666 (t80) cc_final: 0.8432 (t80)
REVERT: E  348 ASP cc_start: 0.8215 (t0) cc_final: 0.7943 (m-30)
REVERT: G  348 ASP cc_start: 0.7698 (t0) cc_final: 0.7386 (m-30)
REVERT: I  351 GLN cc_start: 0.7446 (tt0) cc_final: 0.7144 (tm-30)
  outliers start: 6
  outliers final: 5
  residues processed: 90
  average time/residue: 0.1860
  time to fit residues: 22.0392
Evaluate side-chains
  66 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  307 GLN
Chi-restraints excluded: chain B residue  314 ASP
Chi-restraints excluded: chain D residue  314 ASP
Chi-restraints excluded: chain F residue  314 ASP
Chi-restraints excluded: chain H residue  314 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0370
   chunk 3 optimal weight:    5.9990
   chunk 41 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 55 optimal weight:   10.0000
   chunk 63 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 52 optimal weight:    9.9990
   overall best weight:    2.7864

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.089042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.076873 restraints weight = 72578.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.4180 rms_B_bonded: 6.78
r_work: 0.4071 rms_B_bonded: 6.11 restraints_weight: 2.0000
r_work (final): 0.4071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6367
moved from start:          0.5324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   5830  Z= 0.135
  Angle     :  0.628   6.057   7800  Z= 0.338
  Chirality :  0.051   0.131    880
  Planarity :  0.003   0.027    990
  Dihedral  :  5.252  17.194    770
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 11.21 %
    Favored  : 88.18 %
  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: -2.48 (0.24), residues: 730
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (0.18), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 349 
 TYR   0.007   0.002   TYR B 310 
 PHE   0.013   0.001   PHE I 378 
 HIS   0.003   0.001   HIS H 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 5830)
  covalent geometry    : angle       0.62843 ( 7800)
  hydrogen bonds       : bond        0.04738 (  160)
  hydrogen bonds       : angle       6.29479 (  480)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  358 ASP cc_start: 0.8644 (p0) cc_final: 0.8218 (m-30)
REVERT: B  378 PHE cc_start: 0.8254 (t80) cc_final: 0.7711 (t80)
REVERT: C  348 ASP cc_start: 0.8112 (t0) cc_final: 0.7862 (m-30)
REVERT: C  372 GLU cc_start: 0.6901 (mp0) cc_final: 0.6593 (mp0)
REVERT: E  348 ASP cc_start: 0.8272 (t0) cc_final: 0.8050 (m-30)
REVERT: I  351 GLN cc_start: 0.7491 (tt0) cc_final: 0.7227 (tm-30)
  outliers start: 4
  outliers final: 3
  residues processed: 70
  average time/residue: 0.1679
  time to fit residues: 16.1284
Evaluate side-chains
  61 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  307 GLN
Chi-restraints excluded: chain D residue  346 PHE
Chi-restraints excluded: chain F residue  357 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 17 optimal weight:    9.9990
   chunk 26 optimal weight:   10.0000
   chunk 13 optimal weight:    7.9990
   chunk 24 optimal weight:   10.0000
   chunk 61 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 8 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
F 362 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.084968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.074163 restraints weight = 71268.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.4266 rms_B_bonded: 5.80
r_work: 0.4193 rms_B_bonded: 5.06 restraints_weight: 2.0000
r_work (final): 0.4193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.6143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   5830  Z= 0.222
  Angle     :  0.659   5.723   7800  Z= 0.353
  Chirality :  0.051   0.135    880
  Planarity :  0.004   0.021    990
  Dihedral  :  5.533  17.980    770
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.45 %
    Favored  : 90.55 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 10.15 %
    Favored  : 87.88 %
  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: -2.82 (0.24), residues: 730
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.18), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 349 
 TYR   0.007   0.002   TYR J 310 
 PHE   0.007   0.001   PHE F 378 
 HIS   0.007   0.002   HIS C 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 5830)
  covalent geometry    : angle       0.65875 ( 7800)
  hydrogen bonds       : bond        0.04789 (  160)
  hydrogen bonds       : angle       6.12692 (  480)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  378 PHE cc_start: 0.8595 (t80) cc_final: 0.8284 (t80)
REVERT: H  378 PHE cc_start: 0.8294 (t80) cc_final: 0.8083 (t80)
REVERT: I  351 GLN cc_start: 0.8013 (tt0) cc_final: 0.7592 (tm-30)
REVERT: J  308 ILE cc_start: 0.8556 (pt) cc_final: 0.8278 (mp)
  outliers start: 13
  outliers final: 10
  residues processed: 60
  average time/residue: 0.1187
  time to fit residues: 10.7306
Evaluate side-chains
  54 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  307 GLN
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue  346 PHE
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain G residue  357 LEU
Chi-restraints excluded: chain G residue  358 ASP
Chi-restraints excluded: chain I residue  348 ASP
Chi-restraints excluded: chain I residue  357 LEU
Chi-restraints excluded: chain J residue  346 PHE
Chi-restraints excluded: chain J residue  357 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 63 optimal weight:    8.9990
   chunk 23 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 33 optimal weight:    7.9990
   chunk 28 optimal weight:    9.9990
   chunk 50 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 60 optimal weight:    9.9990
   chunk 36 optimal weight:    8.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
G 329 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.083707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.071968 restraints weight = 76112.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.4115 rms_B_bonded: 6.43
r_work: 0.4014 rms_B_bonded: 5.86 restraints_weight: 2.0000
r_work (final): 0.4014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6723
moved from start:          0.6659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5830  Z= 0.193
  Angle     :  0.608   5.571   7800  Z= 0.324
  Chirality :  0.050   0.133    880
  Planarity :  0.003   0.023    990
  Dihedral  :  5.405  17.298    770
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 11.06 %
    Favored  : 87.12 %
  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: -3.01 (0.24), residues: 730
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.28 (0.18), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E 349 
 TYR   0.008   0.002   TYR J 310 
 PHE   0.011   0.002   PHE E 378 
 HIS   0.004   0.001   HIS J 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 5830)
  covalent geometry    : angle       0.60839 ( 7800)
  hydrogen bonds       : bond        0.04469 (  160)
  hydrogen bonds       : angle       5.81273 (  480)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  378 PHE cc_start: 0.8640 (t80) cc_final: 0.8301 (t80)
REVERT: G  340 LYS cc_start: 0.7536 (mttt) cc_final: 0.7246 (tptp)
REVERT: I  351 GLN cc_start: 0.7681 (tt0) cc_final: 0.7341 (tm-30)
REVERT: J  308 ILE cc_start: 0.8645 (pt) cc_final: 0.8317 (mp)
  outliers start: 12
  outliers final: 11
  residues processed: 49
  average time/residue: 0.1162
  time to fit residues: 8.4743
Evaluate side-chains
  50 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue  346 PHE
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain G residue  358 ASP
Chi-restraints excluded: chain G residue  371 ILE
Chi-restraints excluded: chain H residue  308 ILE
Chi-restraints excluded: chain H residue  346 PHE
Chi-restraints excluded: chain J residue  346 PHE
Chi-restraints excluded: chain J residue  357 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 66 optimal weight:    7.9990
   chunk 64 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9980
   chunk 4 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 38 optimal weight:    9.9990
   chunk 53 optimal weight:   10.0000
   chunk 63 optimal weight:    2.9990
   overall best weight:    4.9988

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

Flipped N/Q/H residues before XYZ refinement:
B 362 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.083965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.072518 restraints weight = 73854.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.4138 rms_B_bonded: 6.17
r_work: 0.4040 rms_B_bonded: 5.67 restraints_weight: 2.0000
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6881
moved from start:          0.6983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5830  Z= 0.182
  Angle     :  0.578   5.443   7800  Z= 0.307
  Chirality :  0.049   0.132    880
  Planarity :  0.003   0.025    990
  Dihedral  :  5.331  16.043    770
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 12.27 %
    Favored  : 85.76 %
  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: -3.11 (0.24), residues: 730
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.36 (0.18), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 349 
 TYR   0.006   0.002   TYR B 310 
 PHE   0.008   0.001   PHE F 346 
 HIS   0.003   0.001   HIS J 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 5830)
  covalent geometry    : angle       0.57798 ( 7800)
  hydrogen bonds       : bond        0.04324 (  160)
  hydrogen bonds       : angle       5.62285 (  480)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 36
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: B  378 PHE cc_start: 0.8787 (t80) cc_final: 0.8278 (t80)
REVERT: F  346 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.8086 (p90)
REVERT: G  340 LYS cc_start: 0.7673 (mttt) cc_final: 0.7324 (tptp)
REVERT: I  351 GLN cc_start: 0.7855 (tt0) cc_final: 0.7334 (tm-30)
REVERT: J  308 ILE cc_start: 0.8647 (pt) cc_final: 0.8345 (mp)
  outliers start: 13
  outliers final: 11
  residues processed: 45
  average time/residue: 0.1289
  time to fit residues: 8.5499
Evaluate side-chains
  44 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 32
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue  346 PHE
Chi-restraints excluded: chain F residue  346 PHE
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain F residue  371 ILE
Chi-restraints excluded: chain G residue  357 LEU
Chi-restraints excluded: chain G residue  358 ASP
Chi-restraints excluded: chain H residue  346 PHE
Chi-restraints excluded: chain I residue  348 ASP
Chi-restraints excluded: chain J residue  346 PHE
Chi-restraints excluded: chain J residue  357 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 11 optimal weight:    8.9990
   chunk 52 optimal weight:    9.9990
   chunk 43 optimal weight:    9.9990
   chunk 12 optimal weight:    2.9990
   chunk 51 optimal weight:    8.9990
   chunk 64 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   chunk 22 optimal weight:   20.0000
   chunk 59 optimal weight:    9.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.082462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.071168 restraints weight = 75706.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.4091 rms_B_bonded: 6.10
r_work: 0.3992 rms_B_bonded: 5.71 restraints_weight: 2.0000
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6756
moved from start:          0.7413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   5830  Z= 0.248
  Angle     :  0.641   5.921   7800  Z= 0.342
  Chirality :  0.049   0.143    880
  Planarity :  0.004   0.028    990
  Dihedral  :  5.739  16.533    770
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.90 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 12.27 %
    Favored  : 85.15 %
  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: -3.31 (0.24), residues: 730
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.52 (0.18), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 349 
 TYR   0.008   0.002   TYR B 310 
 PHE   0.010   0.002   PHE F 346 
 HIS   0.004   0.001   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 ( 5830)
  covalent geometry    : angle       0.64055 ( 7800)
  hydrogen bonds       : bond        0.04896 (  160)
  hydrogen bonds       : angle       5.78755 (  480)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 28
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
REVERT: B  378 PHE cc_start: 0.8674 (t80) cc_final: 0.8324 (t80)
REVERT: F  346 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7949 (p90)
REVERT: I  351 GLN cc_start: 0.7656 (tt0) cc_final: 0.7194 (tm-30)
  outliers start: 17
  outliers final: 14
  residues processed: 40
  average time/residue: 0.1067
  time to fit residues: 6.7557
Evaluate side-chains
  43 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 28
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue  346 PHE
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain E residue  357 LEU
Chi-restraints excluded: chain F residue  346 PHE
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain F residue  371 ILE
Chi-restraints excluded: chain G residue  357 LEU
Chi-restraints excluded: chain G residue  358 ASP
Chi-restraints excluded: chain H residue  308 ILE
Chi-restraints excluded: chain H residue  325 LEU
Chi-restraints excluded: chain H residue  346 PHE
Chi-restraints excluded: chain I residue  348 ASP
Chi-restraints excluded: chain J residue  346 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 55 optimal weight:   20.0000
   chunk 6 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 59 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   chunk 5 optimal weight:    3.9990
   chunk 54 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.082402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.070893 restraints weight = 76673.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.4100 rms_B_bonded: 6.27
r_work: 0.4002 rms_B_bonded: 5.80 restraints_weight: 2.0000
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6777
moved from start:          0.7510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5830  Z= 0.173
  Angle     :  0.567   5.397   7800  Z= 0.302
  Chirality :  0.049   0.133    880
  Planarity :  0.003   0.030    990
  Dihedral  :  5.409  15.203    770
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.18 %
    Favored  : 85.00 %
  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: -3.37 (0.24), residues: 730
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.56 (0.18), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 349 
 TYR   0.007   0.002   TYR B 310 
 PHE   0.008   0.001   PHE F 346 
 HIS   0.003   0.001   HIS I 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 5830)
  covalent geometry    : angle       0.56676 ( 7800)
  hydrogen bonds       : bond        0.04310 (  160)
  hydrogen bonds       : angle       5.52510 (  480)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 30
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: B  378 PHE cc_start: 0.8633 (t80) cc_final: 0.8209 (t80)
REVERT: F  346 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7963 (p90)
REVERT: I  351 GLN cc_start: 0.7758 (tt0) cc_final: 0.7351 (tm-30)
  outliers start: 12
  outliers final: 10
  residues processed: 39
  average time/residue: 0.0979
  time to fit residues: 6.1047
Evaluate side-chains
  39 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 28
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue  346 PHE
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain F residue  346 PHE
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain F residue  371 ILE
Chi-restraints excluded: chain G residue  357 LEU
Chi-restraints excluded: chain G residue  358 ASP
Chi-restraints excluded: chain H residue  346 PHE
Chi-restraints excluded: chain J residue  346 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 28 optimal weight:   10.0000
   chunk 68 optimal weight:   10.0000
   chunk 41 optimal weight:   10.0000
   chunk 43 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   chunk 64 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.082998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.071576 restraints weight = 76156.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.4120 rms_B_bonded: 6.29
r_work: 0.4016 rms_B_bonded: 5.82 restraints_weight: 2.0000
r_work (final): 0.4016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6720
moved from start:          0.7653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5830  Z= 0.151
  Angle     :  0.546   5.360   7800  Z= 0.290
  Chirality :  0.050   0.132    880
  Planarity :  0.003   0.028    990
  Dihedral  :  5.180  14.280    770
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 13.18 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.42 (0.23), residues: 730
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.60 (0.18), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 349 
 TYR   0.007   0.002   TYR C 310 
 PHE   0.008   0.001   PHE F 346 
 HIS   0.003   0.001   HIS I 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 5830)
  covalent geometry    : angle       0.54635 ( 7800)
  hydrogen bonds       : bond        0.04017 (  160)
  hydrogen bonds       : angle       5.33784 (  480)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 32
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
REVERT: B  378 PHE cc_start: 0.8608 (t80) cc_final: 0.8186 (t80)
REVERT: F  346 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7958 (p90)
REVERT: I  351 GLN cc_start: 0.7680 (tt0) cc_final: 0.7294 (tm-30)
  outliers start: 13
  outliers final: 12
  residues processed: 42
  average time/residue: 0.0986
  time to fit residues: 6.7252
Evaluate side-chains
  45 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 32
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 ASN
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue  346 PHE
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain F residue  346 PHE
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain F residue  371 ILE
Chi-restraints excluded: chain G residue  357 LEU
Chi-restraints excluded: chain G residue  358 ASP
Chi-restraints excluded: chain H residue  346 PHE
Chi-restraints excluded: chain J residue  346 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 29 optimal weight:    8.9990
   chunk 33 optimal weight:    9.9990
   chunk 51 optimal weight:   10.0000
   chunk 41 optimal weight:   20.0000
   chunk 5 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 57 optimal weight:    7.9990
   chunk 25 optimal weight:    8.9990
   chunk 7 optimal weight:   20.0000
   chunk 64 optimal weight:   20.0000
   overall best weight:    7.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 327 ASN
A 329 HIS
B 329 HIS
B 359 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.081546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.070308 restraints weight = 78455.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.4106 rms_B_bonded: 6.22
r_work: 0.4002 rms_B_bonded: 5.75 restraints_weight: 2.0000
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6784
moved from start:          0.7829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   5830  Z= 0.263
  Angle     :  0.631   5.877   7800  Z= 0.336
  Chirality :  0.050   0.141    880
  Planarity :  0.004   0.029    990
  Dihedral  :  5.602  15.407    770
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.55 %
    Favored  : 89.45 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 13.48 %
    Favored  : 84.55 %
  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: -3.63 (0.23), residues: 730
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.76 (0.18), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 349 
 TYR   0.007   0.002   TYR B 310 
 PHE   0.009   0.002   PHE F 346 
 HIS   0.005   0.001   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00548 ( 5830)
  covalent geometry    : angle       0.63058 ( 7800)
  hydrogen bonds       : bond        0.04804 (  160)
  hydrogen bonds       : angle       5.48220 (  480)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 28
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: B  378 PHE cc_start: 0.8648 (t80) cc_final: 0.8232 (t80)
REVERT: F  346 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7962 (p90)
REVERT: I  351 GLN cc_start: 0.7661 (tt0) cc_final: 0.7272 (tm-30)
  outliers start: 13
  outliers final: 12
  residues processed: 38
  average time/residue: 0.1072
  time to fit residues: 6.4575
Evaluate side-chains
  40 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 27
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 ASN
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue  346 PHE
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain F residue  346 PHE
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain F residue  371 ILE
Chi-restraints excluded: chain G residue  357 LEU
Chi-restraints excluded: chain G residue  358 ASP
Chi-restraints excluded: chain H residue  346 PHE
Chi-restraints excluded: chain J residue  346 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 63 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 60 optimal weight:   10.0000
   chunk 40 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    2.7186

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.081736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.070455 restraints weight = 77582.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.4151 rms_B_bonded: 6.20
r_work: 0.4049 rms_B_bonded: 5.50 restraints_weight: 2.0000
r_work (final): 0.4049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6745
moved from start:          0.7833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.144   5830  Z= 0.255
  Angle     :  1.042  59.139   7800  Z= 0.627
  Chirality :  0.051   0.323    880
  Planarity :  0.004   0.044    990
  Dihedral  :  5.633  15.944    770
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.14 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 13.64 %
    Favored  : 84.09 %
  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: -3.65 (0.23), residues: 730
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.77 (0.18), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 349 
 TYR   0.007   0.002   TYR B 310 
 PHE   0.008   0.002   PHE F 346 
 HIS   0.004   0.001   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 ( 5830)
  covalent geometry    : angle       1.04180 ( 7800)
  hydrogen bonds       : bond        0.04626 (  160)
  hydrogen bonds       : angle       5.48169 (  480)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2917.32 seconds
wall clock time: 50 minutes 30.51 seconds (3030.51 seconds total)