Starting phenix.real_space_refine
on Sun Apr  5 00:30:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9o8h_70227/04_2026/9o8h_70227.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9o8h_70227/04_2026/9o8h_70227.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9o8h_70227/04_2026/9o8h_70227.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9o8h_70227/04_2026/9o8h_70227.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9o8h_70227/04_2026/9o8h_70227.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9o8h_70227/04_2026/9o8h_70227.map"
  }
  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=  -0.000 sd=   1.000
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      20      5.16       5
     Cl     10      4.86       5
     C    3940      2.51       5
     N    1200      2.21       5
     O    1220      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6390
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 638
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 70, 514
          Classifications: {'peptide': 70}
          Link IDs: {'PTRANS': 3, 'TRANS': 66}
      Conformer: "B"
        Number of residues, atoms: 70, 514
          Classifications: {'peptide': 70}
          Link IDs: {'PTRANS': 3, 'TRANS': 66}
          bond proxies already assigned to first conformer: 393
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J
  Residues with excluded nonbonded symmetry interactions: 170
    residue:
      pdb=" N  AGLY A 326 " occ=0.50
      ... (6 atoms not shown)
      pdb=" O  BGLY A 326 " occ=0.50
    residue:
      pdb=" N  AASN A 327 " occ=0.50
      ... (14 atoms not shown)
      pdb=" ND2BASN A 327 " occ=0.50
    residue:
      pdb=" N  AILE A 328 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CD1BILE A 328 " occ=0.50
    residue:
      pdb=" N  AHIS A 329 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS A 329 " occ=0.50
    residue:
      pdb=" N  AHIS A 330 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS A 330 " occ=0.50
    residue:
      pdb=" N  ALYS A 331 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS A 331 " occ=0.50
    residue:
      pdb=" N  APRO A 332 " occ=0.50
      ... (12 atoms not shown)
      pdb=" CD BPRO A 332 " occ=0.50
    residue:
      pdb=" N  AGLY A 333 " occ=0.50
      ... (6 atoms not shown)
      pdb=" O  BGLY A 333 " occ=0.50
    residue:
      pdb=" N  AGLY A 334 " occ=0.50
      ... (6 atoms not shown)
      pdb=" O  BGLY A 334 " occ=0.50
    residue:
      pdb=" N  AGLY A 335 " occ=0.50
      ... (6 atoms not shown)
      pdb=" O  BGLY A 335 " occ=0.50
    residue:
      pdb=" N  AGLN A 336 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NE2BGLN A 336 " occ=0.50
    residue:
      pdb=" N  AVAL A 337 " occ=0.50
      ... (12 atoms not shown)
      pdb=" CG2BVAL A 337 " occ=0.50
    ... (remaining 158 not shown)
  Time building chain proxies: 0.69, per 1000 atoms: 0.11
  Number of scatterers: 6390
  At special positions: 0
  Unit cell: (82.39, 123.05, 46.01, 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)
     Cl     10     17.00
     S      20     16.00
     O    1220      8.00
     N    1200      7.00
     C    3940      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 322 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 322 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 291 " - pdb=" SG  CYS C 322 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 291 " - pdb=" SG  CYS D 322 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 291 " - pdb=" SG  CYS E 322 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 291 " - pdb=" SG  CYS F 322 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 291 " - pdb=" SG  CYS G 322 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H 291 " - pdb=" SG  CYS H 322 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 291 " - pdb=" SG  CYS I 322 " distance=2.02
    Simple disulfide: pdb=" SG  CYS J 291 " - pdb=" SG  CYS J 322 " distance=2.02

  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: 0.43
  Conformation dependent library (CDL) restraints added in 412.7 milliseconds
  

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1460

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 55.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'H' and resid 274 through 283
      removed outlier: 6.561A  pdb=" N   LYS A 274 " --> pdb=" O   VAL E 275 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   ILE E 277 " --> pdb=" O   LYS A 274 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   GLN A 276 " --> pdb=" O   ILE E 277 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   ASN E 279 " --> pdb=" O   GLN A 276 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   ILE A 278 " --> pdb=" O   ASN E 279 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   LYS E 281 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   LYS A 280 " --> pdb=" O   LYS E 281 " (cutoff:3.500A)
      removed outlier: 7.895A  pdb=" N   ASP E 283 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   LEU A 282 " --> pdb=" O   ASP E 283 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   LYS E 274 " --> pdb=" O   VAL I 275 " (cutoff:3.500A)
      removed outlier: 7.969A  pdb=" N   ILE I 277 " --> pdb=" O   LYS E 274 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   GLN E 276 " --> pdb=" O   ILE I 277 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   ASN I 279 " --> pdb=" O   GLN E 276 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   ILE E 278 " --> pdb=" O   ASN I 279 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   LYS I 281 " --> pdb=" O   ILE E 278 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   LYS E 280 " --> pdb=" O   LYS I 281 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   ASP I 283 " --> pdb=" O   LYS E 280 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   LEU E 282 " --> pdb=" O   ASP I 283 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 294 through 298
      removed outlier: 8.899A  pdb=" N   LYS D 294 " --> pdb=" O   ASP H 295 " (cutoff:3.500A)
      removed outlier: 9.342A  pdb=" N   ILE H 297 " --> pdb=" O   LYS D 294 " (cutoff:3.500A)
      removed outlier: 5.633A  pdb=" N   ASN D 296 " --> pdb=" O   ILE H 297 " (cutoff:3.500A)
      removed outlier: 8.905A  pdb=" N   LYS A 294 " --> pdb=" O   ASP D 295 " (cutoff:3.500A)
      removed outlier: 9.350A  pdb=" N   ILE D 297 " --> pdb=" O   LYS A 294 " (cutoff:3.500A)
      removed outlier: 5.638A  pdb=" N   ASN A 296 " --> pdb=" O   ILE D 297 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   ASP A 295 " --> pdb=" O   LYS E 294 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   ASN E 296 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   ASP E 295 " --> pdb=" O   LYS I 294 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   ASN I 296 " --> pdb=" O   ASP E 295 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 305 through 310
      removed outlier: 6.301A  pdb=" N   SER D 305 " --> pdb=" O   VAL H 306 " (cutoff:3.500A)
      removed outlier: 7.998A  pdb=" N   ILE H 308 " --> pdb=" O   SER D 305 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   GLN D 307 " --> pdb=" O   ILE H 308 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   TYR H 310 " --> pdb=" O   GLN D 307 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   VAL D 309 " --> pdb=" O   TYR H 310 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   SER A 305 " --> pdb=" O   VAL D 306 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   ILE D 308 " --> pdb=" O   SER A 305 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   GLN A 307 " --> pdb=" O   ILE D 308 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   TYR D 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   VAL A 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 313 through 328
      removed outlier: 5.413A  pdb=" N   ASP A 314 " --> pdb=" O   LEU E 315 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   LYS E 317 " --> pdb=" O   ASP A 314 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   SER A 316 " --> pdb=" O   LYS E 317 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   THR E 319 " --> pdb=" O   SER A 316 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   VAL A 318 " --> pdb=" O   THR E 319 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   LYS E 321 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 5.792A  pdb=" N   SER A 320 " --> pdb=" O   LYS E 321 " (cutoff:3.500A)
      removed outlier: 7.382A  pdb=" N   GLY E 323 " --> pdb=" O   SER A 320 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   CYS A 322 " --> pdb=" O   GLY E 323 " (cutoff:3.500A)
      removed outlier: 7.790A  pdb=" N   LEU E 325 " --> pdb=" O   CYS A 322 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   SER A 324 " --> pdb=" O   LEU E 325 " (cutoff:3.500A)
      removed outlier: 7.647A  pdb=" N  AASN E 327 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N  AGLY A 326 " --> pdb=" O  AASN E 327 " (cutoff:3.500A)
      removed outlier: 5.411A  pdb=" N   ASP E 314 " --> pdb=" O   LEU I 315 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   LYS I 317 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   SER E 316 " --> pdb=" O   LYS I 317 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   THR I 319 " --> pdb=" O   SER E 316 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   VAL E 318 " --> pdb=" O   THR I 319 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   LYS I 321 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
      removed outlier: 5.794A  pdb=" N   SER E 320 " --> pdb=" O   LYS I 321 " (cutoff:3.500A)
      removed outlier: 7.385A  pdb=" N   GLY I 323 " --> pdb=" O   SER E 320 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   CYS E 322 " --> pdb=" O   GLY I 323 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   LEU I 325 " --> pdb=" O   CYS E 322 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   SER E 324 " --> pdb=" O   LEU I 325 " (cutoff:3.500A)
      removed outlier: 7.652A  pdb=" N  AASN I 327 " --> pdb=" O   SER E 324 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N  AGLY E 326 " --> pdb=" O  AASN I 327 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 335 through 341
      removed outlier: 4.297A  pdb=" N  BGLN D 336 " --> pdb=" O  BGLY H 335 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N  BGLN A 336 " --> pdb=" O  BGLY D 335 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N  AGLY A 335 " --> pdb=" O  AGLN E 336 " (cutoff:3.500A)
      removed outlier: 8.602A  pdb=" N  AGLU E 338 " --> pdb=" O  AGLY A 335 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N  AVAL A 337 " --> pdb=" O  AGLU E 338 " (cutoff:3.500A)
      removed outlier: 8.095A  pdb=" N  ALYS E 340 " --> pdb=" O  AVAL A 337 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N  AVAL A 339 " --> pdb=" O  ALYS E 340 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N  AGLY E 335 " --> pdb=" O  AGLN I 336 " (cutoff:3.500A)
      removed outlier: 8.604A  pdb=" N  AGLU I 338 " --> pdb=" O  AGLY E 335 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N  AVAL E 337 " --> pdb=" O  AGLU I 338 " (cutoff:3.500A)
      removed outlier: 8.098A  pdb=" N  ALYS I 340 " --> pdb=" O  AVAL E 337 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N  AVAL E 339 " --> pdb=" O  ALYS I 340 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 274 through 283
      removed outlier: 6.561A  pdb=" N   LYS B 274 " --> pdb=" O   VAL C 275 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   ILE C 277 " --> pdb=" O   LYS B 274 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   GLN B 276 " --> pdb=" O   ILE C 277 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   ASN C 279 " --> pdb=" O   GLN B 276 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   ILE B 278 " --> pdb=" O   ASN C 279 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   LYS C 281 " --> pdb=" O   ILE B 278 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   LYS B 280 " --> pdb=" O   LYS C 281 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   ASP C 283 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   LEU B 282 " --> pdb=" O   ASP C 283 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LYS C 274 " --> pdb=" O   VAL G 275 " (cutoff:3.500A)
      removed outlier: 7.968A  pdb=" N   ILE G 277 " --> pdb=" O   LYS C 274 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   GLN C 276 " --> pdb=" O   ILE G 277 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   ASN G 279 " --> pdb=" O   GLN C 276 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   ILE C 278 " --> pdb=" O   ASN G 279 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   LYS G 281 " --> pdb=" O   ILE C 278 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   LYS C 280 " --> pdb=" O   LYS G 281 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   ASP G 283 " --> pdb=" O   LYS C 280 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   LEU C 282 " --> pdb=" O   ASP G 283 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LYS G 274 " --> pdb=" O   VAL J 275 " (cutoff:3.500A)
      removed outlier: 7.968A  pdb=" N   ILE J 277 " --> pdb=" O   LYS G 274 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   GLN G 276 " --> pdb=" O   ILE J 277 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   ASN J 279 " --> pdb=" O   GLN G 276 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   ILE G 278 " --> pdb=" O   ASN J 279 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   LYS J 281 " --> pdb=" O   ILE G 278 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   LYS G 280 " --> pdb=" O   LYS J 281 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   ASP J 283 " --> pdb=" O   LYS G 280 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   LEU G 282 " --> pdb=" O   ASP J 283 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 294 through 298
      removed outlier: 8.899A  pdb=" N   LYS B 294 " --> pdb=" O   ASP F 295 " (cutoff:3.500A)
      removed outlier: 9.342A  pdb=" N   ILE F 297 " --> pdb=" O   LYS B 294 " (cutoff:3.500A)
      removed outlier: 5.632A  pdb=" N   ASN B 296 " --> pdb=" O   ILE F 297 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   ASP B 295 " --> pdb=" O   LYS C 294 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   ASN C 296 " --> pdb=" O   ASP B 295 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   ASP C 295 " --> pdb=" O   LYS G 294 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   ASN G 296 " --> pdb=" O   ASP C 295 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   ASP G 295 " --> pdb=" O   LYS J 294 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   ASN J 296 " --> pdb=" O   ASP G 295 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 305 through 310
      removed outlier: 6.300A  pdb=" N   SER B 305 " --> pdb=" O   VAL F 306 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   ILE F 308 " --> pdb=" O   SER B 305 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   GLN B 307 " --> pdb=" O   ILE F 308 " (cutoff:3.500A)
      removed outlier: 7.865A  pdb=" N   TYR F 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   VAL B 309 " --> pdb=" O   TYR F 310 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 313 through 328
      removed outlier: 5.420A  pdb=" N   ASP B 314 " --> pdb=" O   LEU C 315 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   LYS C 317 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   SER B 316 " --> pdb=" O   LYS C 317 " (cutoff:3.500A)
      removed outlier: 7.587A  pdb=" N   THR C 319 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   VAL B 318 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 7.668A  pdb=" N   LYS C 321 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 5.803A  pdb=" N   SER B 320 " --> pdb=" O   LYS C 321 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   GLY C 323 " --> pdb=" O   SER B 320 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   CYS B 322 " --> pdb=" O   GLY C 323 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   LEU C 325 " --> pdb=" O   CYS B 322 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   SER B 324 " --> pdb=" O   LEU C 325 " (cutoff:3.500A)
      removed outlier: 7.660A  pdb=" N  AASN C 327 " --> pdb=" O   SER B 324 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N  AGLY B 326 " --> pdb=" O  AASN C 327 " (cutoff:3.500A)
      removed outlier: 5.421A  pdb=" N   ASP C 314 " --> pdb=" O   LEU G 315 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   LYS G 317 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   SER C 316 " --> pdb=" O   LYS G 317 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   THR G 319 " --> pdb=" O   SER C 316 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   VAL C 318 " --> pdb=" O   THR G 319 " (cutoff:3.500A)
      removed outlier: 7.667A  pdb=" N   LYS G 321 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 5.804A  pdb=" N   SER C 320 " --> pdb=" O   LYS G 321 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   GLY G 323 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   CYS C 322 " --> pdb=" O   GLY G 323 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   LEU G 325 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   SER C 324 " --> pdb=" O   LEU G 325 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N  AASN G 327 " --> pdb=" O   SER C 324 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N  AGLY C 326 " --> pdb=" O  AASN G 327 " (cutoff:3.500A)
      removed outlier: 5.420A  pdb=" N   ASP G 314 " --> pdb=" O   LEU J 315 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   LYS J 317 " --> pdb=" O   ASP G 314 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   SER G 316 " --> pdb=" O   LYS J 317 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   THR J 319 " --> pdb=" O   SER G 316 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   VAL G 318 " --> pdb=" O   THR J 319 " (cutoff:3.500A)
      removed outlier: 7.668A  pdb=" N   LYS J 321 " --> pdb=" O   VAL G 318 " (cutoff:3.500A)
      removed outlier: 5.803A  pdb=" N   SER G 320 " --> pdb=" O   LYS J 321 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   GLY J 323 " --> pdb=" O   SER G 320 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   CYS G 322 " --> pdb=" O   GLY J 323 " (cutoff:3.500A)
      removed outlier: 7.800A  pdb=" N   LEU J 325 " --> pdb=" O   CYS G 322 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   SER G 324 " --> pdb=" O   LEU J 325 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N  AASN J 327 " --> pdb=" O   SER G 324 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N  AGLY G 326 " --> pdb=" O  AASN J 327 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 335 through 341
      removed outlier: 4.298A  pdb=" N  BGLN B 336 " --> pdb=" O  BGLY F 335 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N  AGLY B 335 " --> pdb=" O  AGLN C 336 " (cutoff:3.500A)
      removed outlier: 8.604A  pdb=" N  AGLU C 338 " --> pdb=" O  AGLY B 335 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N  AVAL B 337 " --> pdb=" O  AGLU C 338 " (cutoff:3.500A)
      removed outlier: 8.096A  pdb=" N  ALYS C 340 " --> pdb=" O  AVAL B 337 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N  AVAL B 339 " --> pdb=" O  ALYS C 340 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N  AGLY C 335 " --> pdb=" O  AGLN G 336 " (cutoff:3.500A)
      removed outlier: 8.604A  pdb=" N  AGLU G 338 " --> pdb=" O  AGLY C 335 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N  AVAL C 337 " --> pdb=" O  AGLU G 338 " (cutoff:3.500A)
      removed outlier: 8.096A  pdb=" N  ALYS G 340 " --> pdb=" O  AVAL C 337 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N  AVAL C 339 " --> pdb=" O  ALYS G 340 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N  AGLY G 335 " --> pdb=" O  AGLN J 336 " (cutoff:3.500A)
      removed outlier: 8.604A  pdb=" N  AGLU J 338 " --> pdb=" O  AGLY G 335 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N  AVAL G 337 " --> pdb=" O  AGLU J 338 " (cutoff:3.500A)
      removed outlier: 8.096A  pdb=" N  ALYS J 340 " --> pdb=" O  AVAL G 337 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N  AVAL G 339 " --> pdb=" O  ALYS J 340 " (cutoff:3.500A)

    149 hydrogen bonds defined for protein.
    447 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: 0.84

  Time building geometry restraints manager: 0.62 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2140
        1.34 -     1.45: 824
        1.45 -     1.57: 3486
        1.57 -     1.68: 0
        1.68 -     1.80: 20
  Bond restraints: 6470
  Sorted by residual:
  bond pdb=" CA  LEU J 315 "
       pdb=" CB  LEU J 315 "
    ideal  model  delta    sigma   weight residual
    1.527  1.443  0.083 1.75e-02 3.27e+03 2.27e+01
  bond pdb=" CA  LEU I 315 "
       pdb=" CB  LEU I 315 "
    ideal  model  delta    sigma   weight residual
    1.527  1.443  0.083 1.75e-02 3.27e+03 2.27e+01
  bond pdb=" CA  LEU G 315 "
       pdb=" CB  LEU G 315 "
    ideal  model  delta    sigma   weight residual
    1.527  1.444  0.083 1.75e-02 3.27e+03 2.26e+01
  bond pdb=" CA  LEU A 315 "
       pdb=" CB  LEU A 315 "
    ideal  model  delta    sigma   weight residual
    1.527  1.444  0.083 1.75e-02 3.27e+03 2.25e+01
  bond pdb=" CA  LEU B 315 "
       pdb=" CB  LEU B 315 "
    ideal  model  delta    sigma   weight residual
    1.527  1.444  0.083 1.75e-02 3.27e+03 2.25e+01
  ... (remaining 6465 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.08: 6787
        1.08 -     2.15: 1400
        2.15 -     3.23: 377
        3.23 -     4.30: 76
        4.30 -     5.38: 10
  Bond angle restraints: 8650
  Sorted by residual:
  angle pdb=" CA  VAL I 318 "
        pdb=" C   VAL I 318 "
        pdb=" O   VAL I 318 "
      ideal   model   delta    sigma   weight residual
     120.53  117.78    2.75 1.07e+00 8.73e-01 6.60e+00
  angle pdb=" CA  VAL E 318 "
        pdb=" C   VAL E 318 "
        pdb=" O   VAL E 318 "
      ideal   model   delta    sigma   weight residual
     120.39  117.72    2.67 1.04e+00 9.25e-01 6.59e+00
  angle pdb=" CA  VAL F 318 "
        pdb=" C   VAL F 318 "
        pdb=" O   VAL F 318 "
      ideal   model   delta    sigma   weight residual
     120.53  117.81    2.72 1.07e+00 8.73e-01 6.49e+00
  angle pdb=" CA  VAL D 318 "
        pdb=" C   VAL D 318 "
        pdb=" O   VAL D 318 "
      ideal   model   delta    sigma   weight residual
     120.39  117.76    2.63 1.04e+00 9.25e-01 6.41e+00
  angle pdb=" CA  VAL C 318 "
        pdb=" C   VAL C 318 "
        pdb=" O   VAL C 318 "
      ideal   model   delta    sigma   weight residual
     120.53  117.83    2.70 1.07e+00 8.73e-01 6.39e+00
  ... (remaining 8645 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.52: 3432
       14.52 -    29.04: 438
       29.04 -    43.56: 70
       43.56 -    58.08: 20
       58.08 -    72.60: 20
  Dihedral angle restraints: 3980
    sinusoidal: 1650
      harmonic: 2330
  Sorted by residual:
  dihedral pdb=" CA  VAL I 313 "
           pdb=" C   VAL I 313 "
           pdb=" N   ASP I 314 "
           pdb=" CA  ASP I 314 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.97  -21.03     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CA  VAL G 313 "
           pdb=" C   VAL G 313 "
           pdb=" N   ASP G 314 "
           pdb=" CA  ASP G 314 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.00  -21.00     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CA  VAL B 313 "
           pdb=" C   VAL B 313 "
           pdb=" N   ASP B 314 "
           pdb=" CA  ASP B 314 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.01  -20.99     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 3977 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 502
       0.044 -    0.088: 252
       0.088 -    0.131: 146
       0.131 -    0.175: 11
       0.175 -    0.219: 39
  Chirality restraints: 950
  Sorted by residual:
  chirality pdb=" CA  VAL D 309 "
            pdb=" N   VAL D 309 "
            pdb=" C   VAL D 309 "
            pdb=" CB  VAL D 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  VAL C 309 "
            pdb=" N   VAL C 309 "
            pdb=" C   VAL C 309 "
            pdb=" CB  VAL C 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  VAL E 309 "
            pdb=" N   VAL E 309 "
            pdb=" C   VAL E 309 "
            pdb=" CB  VAL E 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 947 not shown)

  Planarity restraints: 1130
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 290 "    0.020 2.00e-02 2.50e+03   4.12e-02 1.70e+01
        pdb=" C   LYS B 290 "   -0.071 2.00e-02 2.50e+03
        pdb=" O   LYS B 290 "    0.027 2.00e-02 2.50e+03
        pdb=" N   CYS B 291 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS H 290 "   -0.020 2.00e-02 2.50e+03   4.12e-02 1.70e+01
        pdb=" C   LYS H 290 "    0.071 2.00e-02 2.50e+03
        pdb=" O   LYS H 290 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   CYS H 291 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 290 "   -0.020 2.00e-02 2.50e+03   4.10e-02 1.68e+01
        pdb=" C   LYS A 290 "    0.071 2.00e-02 2.50e+03
        pdb=" O   LYS A 290 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   CYS A 291 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 1127 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1485
        2.80 -     3.32: 5463
        3.32 -     3.85: 10429
        3.85 -     4.37: 10666
        4.37 -     4.90: 23949
  Nonbonded interactions: 51992
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" OG  SER E 316 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OD1 ASP J 314 "
            pdb=" OG  SER J 316 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" OG  SER A 316 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OD1 ASP I 314 "
            pdb=" OG  SER I 316 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" OG  SER D 316 "
     model   vdw
     2.273 3.040
  ... (remaining 51987 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: 0.02
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=0.50 max=1.00 mean=0.81
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:             2.250
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.670
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.000
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
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      :  0.013   0.083   6480  Z= 0.626
  Angle     :  0.987   5.380   8670  Z= 0.589
  Chirality :  0.070   0.219    950
  Planarity :  0.009   0.041   1130
  Dihedral  : 13.735  72.598   2490
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.29 %
    Favored  : 89.71 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 19.18 %
    Favored  : 75.34 %
  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: -3.66 (0.22), residues: 850
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.78 (0.17), residues: 850

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.004   TYR H 310 
 HIS   0.002   0.001   HIS E 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.01287 ( 6470)
  covalent geometry    : angle       0.98369 ( 8650)
  SS BOND              : bond        0.00575 (   10)
  SS BOND              : angle       1.85682 (   20)
  hydrogen bonds       : bond        0.15002 (  149)
  hydrogen bonds       : angle      10.81816 (  447)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 155
  time to evaluate  : 0.178 
Fit side-chains
REVERT: B  311 LYS cc_start: 0.8846 (mttt) cc_final: 0.8525 (mttm)
REVERT: D  280 LYS cc_start: 0.9105 (tttt) cc_final: 0.8815 (tttt)
REVERT: F  290 LYS cc_start: 0.8369 (ttpt) cc_final: 0.7219 (ttpt)
REVERT: F  311 LYS cc_start: 0.8877 (mttt) cc_final: 0.7539 (pttm)
REVERT: H  290 LYS cc_start: 0.8358 (ttpt) cc_final: 0.7231 (ttpt)
REVERT: H  311 LYS cc_start: 0.8771 (mttt) cc_final: 0.8508 (mttm)
REVERT: I  298 LYS cc_start: 0.8914 (mttt) cc_final: 0.7616 (mmtt)
REVERT: I  309 VAL cc_start: 0.9188 (t) cc_final: 0.8922 (p)
REVERT: I  311 LYS cc_start: 0.8591 (mttt) cc_final: 0.7700 (mmtt)
REVERT: J  298 LYS cc_start: 0.8881 (mttt) cc_final: 0.7486 (mmtt)
REVERT: J  311 LYS cc_start: 0.8531 (mttt) cc_final: 0.7534 (mmtt)
  outliers start: 20
  outliers final: 8
  residues processed: 165
  average time/residue: 0.1187
  time to fit residues: 23.7337
Evaluate side-chains
  133 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 125
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain C residue  275 VAL
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain E residue  275 VAL
Chi-restraints excluded: chain F residue  275 VAL
Chi-restraints excluded: chain G residue  275 VAL
Chi-restraints excluded: chain H residue  275 VAL
Chi-restraints excluded: chain I residue  275 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    9.9990
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    7.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 307 GLN
A 327 ASN    B
** A 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 296 ASN
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 327 ASN    B
** B 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 286 ASN
C 296 ASN
** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 327 ASN    B
** C 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 327 ASN    B
** D 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
E 299 HIS
E 327 ASN    B
** E 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
F 296 ASN
** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 327 ASN    B
** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 296 ASN
** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 327 ASN    B
** G 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 327 ASN    B
I 276 GLN
I 279 ASN
I 299 HIS
I 327 ASN    B
** I 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 286 ASN
J 296 ASN
J 299 HIS
J 327 ASN    B
** J 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 23

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4889 r_free = 0.4889 target = 0.219598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.176391 restraints weight = 45620.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.4555 rms_B_bonded: 6.36
r_work: 0.4273 rms_B_bonded: 5.71 restraints_weight: 2.0000
r_work (final): 0.4273
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4270
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4270 r_free = 0.4270    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4269 r_free = 0.4269    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4269
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6480  Z= 0.154
  Angle     :  0.624   4.946   8670  Z= 0.334
  Chirality :  0.051   0.141    950
  Planarity :  0.005   0.031   1130
  Dihedral  :  6.514  28.001    878
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 20.55 %
    Favored  : 75.62 %
  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: -3.60 (0.22), residues: 850
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.74 (0.17), residues: 850

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.015   0.003   TYR C 310 
 HIS   0.001   0.000   HIS D 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 6470)
  covalent geometry    : angle       0.62464 ( 8650)
  SS BOND              : bond        0.00081 (   10)
  SS BOND              : angle       0.45890 (   20)
  hydrogen bonds       : bond        0.03117 (  149)
  hydrogen bonds       : angle       7.07284 (  447)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 142
  time to evaluate  : 0.136 
Fit side-chains
REVERT: B  282 LEU cc_start: 0.9013 (mm) cc_final: 0.8783 (mm)
REVERT: B  290 LYS cc_start: 0.8717 (ttmt) cc_final: 0.8137 (tttm)
REVERT: B  311 LYS cc_start: 0.8872 (mttt) cc_final: 0.8487 (mttm)
REVERT: C  290 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8076 (tttp)
REVERT: D  280 LYS cc_start: 0.9303 (tttt) cc_final: 0.9052 (tttt)
REVERT: F  311 LYS cc_start: 0.8548 (mttt) cc_final: 0.7339 (pttm)
REVERT: F  320 SER cc_start: 0.8855 (m) cc_final: 0.8651 (p)
REVERT: H  311 LYS cc_start: 0.8687 (mttt) cc_final: 0.8439 (mtpt)
REVERT: I  311 LYS cc_start: 0.8573 (mttt) cc_final: 0.8315 (mttm)
REVERT: J  298 LYS cc_start: 0.8608 (mttt) cc_final: 0.7340 (mmtt)
REVERT: J  311 LYS cc_start: 0.8507 (mttt) cc_final: 0.7389 (mmtt)
  outliers start: 6
  outliers final: 5
  residues processed: 144
  average time/residue: 0.0866
  time to fit residues: 15.9735
Evaluate side-chains
  139 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 134
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  275 VAL
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain G residue  275 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 12 optimal weight:    8.9990
   chunk 38 optimal weight:    0.7980
   chunk 24 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 52 optimal weight:    5.9990
   chunk 68 optimal weight:    0.1980
   chunk 20 optimal weight:   30.0000
   chunk 40 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    2.7986

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 307 GLN
** A 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 296 ASN
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 296 ASN
** C 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
F 296 ASN
** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 286 ASN
G 296 ASN
** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 296 ASN
** J 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4806 r_free = 0.4806 target = 0.212733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.168248 restraints weight = 33657.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.4395 rms_B_bonded: 5.38
r_work: 0.4121 rms_B_bonded: 5.23 restraints_weight: 2.0000
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4127
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4127 r_free = 0.4127    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4126 r_free = 0.4126    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4126
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.2376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6480  Z= 0.228
  Angle     :  0.631   5.124   8670  Z= 0.336
  Chirality :  0.051   0.148    950
  Planarity :  0.004   0.027   1130
  Dihedral  :  6.241  29.595    873
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 19.59 %
    Favored  : 75.21 %
  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: -3.58 (0.23), residues: 850
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.72 (0.17), residues: 850

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.016   0.003   TYR C 310 
 HIS   0.002   0.001   HIS H 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 ( 6470)
  covalent geometry    : angle       0.63077 ( 8650)
  SS BOND              : bond        0.00330 (   10)
  SS BOND              : angle       0.76111 (   20)
  hydrogen bonds       : bond        0.02993 (  149)
  hydrogen bonds       : angle       6.63259 (  447)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.207 
Fit side-chains
REVERT: B  282 LEU cc_start: 0.9033 (mm) cc_final: 0.8762 (mm)
REVERT: B  290 LYS cc_start: 0.8792 (ttmt) cc_final: 0.8285 (ttmm)
REVERT: B  311 LYS cc_start: 0.8889 (mttt) cc_final: 0.8501 (mttm)
REVERT: E  282 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8562 (mm)
REVERT: F  311 LYS cc_start: 0.8697 (mttt) cc_final: 0.8455 (mtpt)
REVERT: F  320 SER cc_start: 0.8956 (m) cc_final: 0.8562 (p)
REVERT: H  311 LYS cc_start: 0.8796 (mttt) cc_final: 0.8573 (ttmm)
REVERT: I  296 ASN cc_start: 0.8304 (m-40) cc_final: 0.7181 (p0)
REVERT: J  298 LYS cc_start: 0.8650 (mttt) cc_final: 0.8395 (mtpp)
  outliers start: 16
  outliers final: 12
  residues processed: 132
  average time/residue: 0.0639
  time to fit residues: 11.6869
Evaluate side-chains
  138 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain D residue  282 LEU
Chi-restraints excluded: chain D residue  288 GLN
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  275 VAL
Chi-restraints excluded: chain E residue  282 LEU
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain G residue  275 VAL
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain I residue  275 VAL
Chi-restraints excluded: chain I residue  325 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   chunk 26 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 20 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 307 GLN
** A 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 296 ASN
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 296 ASN
** C 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
F 296 ASN
** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 286 ASN
G 296 ASN
** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 276 GLN
I 286 ASN
** I 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 296 ASN
** J 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4835 r_free = 0.4835 target = 0.214593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.169543 restraints weight = 36867.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.4493 rms_B_bonded: 6.71
r_work: 0.4171 rms_B_bonded: 5.68 restraints_weight: 2.0000
r_work (final): 0.4171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4163
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4163 r_free = 0.4163    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4163 r_free = 0.4163    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4163
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6480  Z= 0.220
  Angle     :  0.612   5.214   8670  Z= 0.325
  Chirality :  0.051   0.151    950
  Planarity :  0.004   0.025   1130
  Dihedral  :  6.062  26.884    873
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 19.86 %
    Favored  : 74.52 %
  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: -3.52 (0.23), residues: 850
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.68 (0.18), residues: 850

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.015   0.003   TYR C 310 
 HIS   0.001   0.001   HIS H 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 6470)
  covalent geometry    : angle       0.61161 ( 8650)
  SS BOND              : bond        0.00287 (   10)
  SS BOND              : angle       0.64221 (   20)
  hydrogen bonds       : bond        0.02675 (  149)
  hydrogen bonds       : angle       6.25784 (  447)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A  276 GLN cc_start: 0.8877 (tt0) cc_final: 0.8634 (tt0)
REVERT: B  290 LYS cc_start: 0.8735 (ttmt) cc_final: 0.8172 (tttm)
REVERT: B  311 LYS cc_start: 0.8841 (mttt) cc_final: 0.8474 (mttm)
REVERT: E  282 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8783 (mm)
REVERT: F  311 LYS cc_start: 0.8674 (mttt) cc_final: 0.8345 (mtpt)
REVERT: F  320 SER cc_start: 0.8967 (m) cc_final: 0.8585 (p)
REVERT: H  311 LYS cc_start: 0.8749 (mttt) cc_final: 0.8480 (mttp)
REVERT: I  296 ASN cc_start: 0.8202 (m-40) cc_final: 0.7208 (p0)
REVERT: J  296 ASN cc_start: 0.8172 (m110) cc_final: 0.7174 (p0)
REVERT: J  298 LYS cc_start: 0.8698 (mttt) cc_final: 0.8395 (mtpp)
  outliers start: 17
  outliers final: 14
  residues processed: 129
  average time/residue: 0.0645
  time to fit residues: 11.8369
Evaluate side-chains
  139 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain C residue  275 VAL
Chi-restraints excluded: chain D residue  282 LEU
Chi-restraints excluded: chain D residue  288 GLN
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  275 VAL
Chi-restraints excluded: chain E residue  282 LEU
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain G residue  275 VAL
Chi-restraints excluded: chain G residue  320 SER
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain I residue  275 VAL
Chi-restraints excluded: chain I residue  325 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 60 optimal weight:    0.3980
   chunk 29 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 47 optimal weight:    8.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 296 ASN
A 307 GLN
** A 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 286 ASN
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 296 ASN
** D 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 296 ASN
** E 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 296 ASN
I 276 GLN
I 296 ASN
** I 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4975 r_free = 0.4975 target = 0.226692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.180897 restraints weight = 36391.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.4581 rms_B_bonded: 6.36
r_work: 0.4254 rms_B_bonded: 6.17 restraints_weight: 2.0000
r_work (final): 0.4254
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4326
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4326 r_free = 0.4326    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4327 r_free = 0.4327    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4327
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.3405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6480  Z= 0.091
  Angle     :  0.540   5.499   8670  Z= 0.281
  Chirality :  0.049   0.133    950
  Planarity :  0.004   0.032   1130
  Dihedral  :  5.528  26.409    873
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.47 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 19.86 %
    Favored  : 74.93 %
  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 (0.24), residues: 850
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.60 (0.18), residues: 850

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.002   TYR C 310 
 HIS   0.001   0.000   HIS C 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 ( 6470)
  covalent geometry    : angle       0.54034 ( 8650)
  SS BOND              : bond        0.00088 (   10)
  SS BOND              : angle       0.44409 (   20)
  hydrogen bonds       : bond        0.01852 (  149)
  hydrogen bonds       : angle       5.63508 (  447)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 140
  time to evaluate  : 0.204 
Fit side-chains
REVERT: D  280 LYS cc_start: 0.9292 (tttt) cc_final: 0.9046 (tttt)
REVERT: F  320 SER cc_start: 0.8927 (m) cc_final: 0.8632 (p)
REVERT: G  282 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8440 (mm)
REVERT: H  280 LYS cc_start: 0.8987 (tttt) cc_final: 0.8661 (tttm)
REVERT: H  290 LYS cc_start: 0.8526 (ttpt) cc_final: 0.7537 (ttpt)
REVERT: H  311 LYS cc_start: 0.8556 (mttt) cc_final: 0.8303 (mttm)
REVERT: I  296 ASN cc_start: 0.8525 (m110) cc_final: 0.7416 (p0)
REVERT: J  296 ASN cc_start: 0.8160 (m110) cc_final: 0.7146 (p0)
REVERT: J  298 LYS cc_start: 0.8391 (mttt) cc_final: 0.8117 (mtpp)
REVERT: J  311 LYS cc_start: 0.7971 (mttt) cc_final: 0.7122 (mmtt)
  outliers start: 14
  outliers final: 10
  residues processed: 142
  average time/residue: 0.0769
  time to fit residues: 14.3942
Evaluate side-chains
  147 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  275 VAL
Chi-restraints excluded: chain G residue  275 VAL
Chi-restraints excluded: chain G residue  282 LEU
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain I residue  325 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 34 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   chunk 69 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   chunk 49 optimal weight:    5.9990
   chunk 27 optimal weight:   20.0000
   chunk 36 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0770
   chunk 43 optimal weight:    3.9990
   chunk 39 optimal weight:    7.9990
   overall best weight:    3.6146

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 296 ASN
** A 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 296 ASN
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 296 ASN
** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 296 ASN
** D 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 296 ASN
** E 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
F 296 ASN
** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 296 ASN
** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
H 296 ASN
I 276 GLN
I 296 ASN
** I 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
J 296 ASN
** J 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4802 r_free = 0.4802 target = 0.211156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.164812 restraints weight = 35584.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.4433 rms_B_bonded: 6.32
r_work: 0.4100 rms_B_bonded: 5.84 restraints_weight: 2.0000
r_work (final): 0.4100
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4075
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4075 r_free = 0.4075    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4075 r_free = 0.4075    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4075
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.3105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   6480  Z= 0.274
  Angle     :  0.638   5.265   8670  Z= 0.340
  Chirality :  0.053   0.218    950
  Planarity :  0.004   0.029   1130
  Dihedral  :  5.955  31.414    873
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  :  8.68 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 21.23 %
    Favored  : 73.01 %
  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: -3.46 (0.24), residues: 850
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.63 (0.19), residues: 850

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.017   0.003   TYR C 310 
 HIS   0.002   0.001   HIS F 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00627 ( 6470)
  covalent geometry    : angle       0.63761 ( 8650)
  SS BOND              : bond        0.00461 (   10)
  SS BOND              : angle       0.91286 (   20)
  hydrogen bonds       : bond        0.02765 (  149)
  hydrogen bonds       : angle       6.12477 (  447)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.210 
Fit side-chains
REVERT: B  290 LYS cc_start: 0.8601 (ttmt) cc_final: 0.8133 (ttmm)
REVERT: B  311 LYS cc_start: 0.8860 (mttt) cc_final: 0.8576 (mttm)
REVERT: F  311 LYS cc_start: 0.8801 (mttt) cc_final: 0.8545 (mttm)
REVERT: F  320 SER cc_start: 0.9011 (m) cc_final: 0.8538 (p)
REVERT: G  276 GLN cc_start: 0.9021 (tt0) cc_final: 0.8724 (tt0)
REVERT: H  311 LYS cc_start: 0.8811 (mttt) cc_final: 0.8571 (mttm)
REVERT: I  296 ASN cc_start: 0.8256 (m-40) cc_final: 0.7252 (p0)
REVERT: J  296 ASN cc_start: 0.8145 (m-40) cc_final: 0.7054 (p0)
REVERT: J  298 LYS cc_start: 0.8522 (mttm) cc_final: 0.8219 (mtpp)
REVERT: J  311 LYS cc_start: 0.8104 (mttt) cc_final: 0.7116 (mmtp)
  outliers start: 18
  outliers final: 14
  residues processed: 134
  average time/residue: 0.0706
  time to fit residues: 13.0245
Evaluate side-chains
  140 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  288 GLN
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  288 GLN
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  288 GLN
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  275 VAL
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain G residue  275 VAL
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain I residue  275 VAL
Chi-restraints excluded: chain I residue  325 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 40 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 7 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 296 ASN
A 307 GLN
** A 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 296 ASN
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 296 ASN
** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 296 ASN
** D 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 296 ASN
** E 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
F 296 ASN
F 299 HIS
** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 296 ASN
** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 296 ASN
I 296 ASN
** I 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 296 ASN
** J 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4983 r_free = 0.4983 target = 0.225970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.180487 restraints weight = 33641.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.4639 rms_B_bonded: 6.05
r_work: 0.4376 rms_B_bonded: 5.53 restraints_weight: 2.0000
r_work (final): 0.4376
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4365
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4365 r_free = 0.4365    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4366 r_free = 0.4366    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4366
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.3697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6480  Z= 0.097
  Angle     :  0.551   5.690   8670  Z= 0.286
  Chirality :  0.050   0.205    950
  Planarity :  0.004   0.034   1130
  Dihedral  :  5.399  28.731    873
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.74 %
    Allowed  :  5.88 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 22.47 %
    Favored  : 72.19 %
  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: -3.33 (0.25), residues: 850
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.53 (0.19), residues: 850

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.002   TYR C 310 
 HIS   0.002   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 6470)
  covalent geometry    : angle       0.55119 ( 8650)
  SS BOND              : bond        0.00089 (   10)
  SS BOND              : angle       0.43489 (   20)
  hydrogen bonds       : bond        0.01821 (  149)
  hydrogen bonds       : angle       5.50803 (  447)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 144
  time to evaluate  : 0.144 
Fit side-chains
REVERT: B  290 LYS cc_start: 0.8546 (ttmt) cc_final: 0.8055 (tttm)
REVERT: D  280 LYS cc_start: 0.9307 (tttt) cc_final: 0.9051 (tttt)
REVERT: E  282 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8678 (mm)
REVERT: F  320 SER cc_start: 0.9008 (m) cc_final: 0.8638 (p)
REVERT: G  290 LYS cc_start: 0.8580 (ttpt) cc_final: 0.8150 (ttmm)
REVERT: H  280 LYS cc_start: 0.9010 (tttt) cc_final: 0.8660 (tttm)
REVERT: H  290 LYS cc_start: 0.8495 (ttpt) cc_final: 0.7577 (ttpt)
REVERT: I  296 ASN cc_start: 0.8344 (m110) cc_final: 0.7326 (p0)
REVERT: J  296 ASN cc_start: 0.8060 (m110) cc_final: 0.7130 (p0)
REVERT: J  298 LYS cc_start: 0.8494 (mttm) cc_final: 0.8158 (mtpp)
REVERT: J  311 LYS cc_start: 0.8035 (mttt) cc_final: 0.7191 (mmtt)
  outliers start: 14
  outliers final: 11
  residues processed: 152
  average time/residue: 0.0770
  time to fit residues: 15.3781
Evaluate side-chains
  155 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 143
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  288 GLN
Chi-restraints excluded: chain B residue  288 GLN
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain E residue  282 LEU
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain G residue  275 VAL
Chi-restraints excluded: chain G residue  320 SER
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain I residue  275 VAL
Chi-restraints excluded: chain I residue  325 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 21 optimal weight:    8.9990
   chunk 16 optimal weight:    9.9990
   chunk 19 optimal weight:    8.9990
   chunk 13 optimal weight:    9.9990
   chunk 50 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 55 optimal weight:    8.9990
   chunk 23 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   overall best weight:    3.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 296 ASN
** A 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 296 ASN
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 GLN
** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 296 ASN
** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 296 ASN
** D 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 296 ASN
** E 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
F 296 ASN
G 296 ASN
** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 296 ASN
I 296 ASN
** I 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
J 296 ASN
** J 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4820 r_free = 0.4820 target = 0.211982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.165531 restraints weight = 38878.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.4454 rms_B_bonded: 6.45
r_work: 0.4113 rms_B_bonded: 6.00 restraints_weight: 2.0000
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4111
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4111 r_free = 0.4111    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4110 r_free = 0.4110    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4110
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.3375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065   6480  Z= 0.270
  Angle     :  0.653   5.845   8670  Z= 0.346
  Chirality :  0.052   0.212    950
  Planarity :  0.004   0.032   1130
  Dihedral  :  5.748  29.959    871
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  8.97 %
    Favored  : 90.15 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 22.60 %
    Favored  : 71.64 %
  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: -3.41 (0.25), residues: 850
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.59 (0.19), residues: 850

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.016   0.003   TYR C 310 
 HIS   0.002   0.001   HIS H 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00628 ( 6470)
  covalent geometry    : angle       0.65231 ( 8650)
  SS BOND              : bond        0.00410 (   10)
  SS BOND              : angle       0.91012 (   20)
  hydrogen bonds       : bond        0.02695 (  149)
  hydrogen bonds       : angle       5.93779 (  447)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 0.204 
Fit side-chains
REVERT: B  290 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8130 (ttmm)
REVERT: B  311 LYS cc_start: 0.8812 (mttt) cc_final: 0.8478 (mttm)
REVERT: F  290 LYS cc_start: 0.8709 (ttpt) cc_final: 0.7446 (ttpt)
REVERT: F  311 LYS cc_start: 0.8784 (mttt) cc_final: 0.7448 (pttm)
REVERT: F  320 SER cc_start: 0.9027 (m) cc_final: 0.8542 (p)
REVERT: H  290 LYS cc_start: 0.8595 (ttpt) cc_final: 0.7825 (ttpt)
REVERT: I  296 ASN cc_start: 0.8247 (m-40) cc_final: 0.7278 (p0)
REVERT: I  298 LYS cc_start: 0.8873 (mttm) cc_final: 0.7501 (mmtt)
REVERT: I  311 LYS cc_start: 0.8323 (mttt) cc_final: 0.7169 (mmtt)
REVERT: J  296 ASN cc_start: 0.8132 (m-40) cc_final: 0.7177 (p0)
  outliers start: 17
  outliers final: 15
  residues processed: 139
  average time/residue: 0.0767
  time to fit residues: 14.3961
Evaluate side-chains
  148 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 133
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  276 GLN
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  288 GLN
Chi-restraints excluded: chain B residue  288 GLN
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain C residue  275 VAL
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain G residue  275 VAL
Chi-restraints excluded: chain G residue  320 SER
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain I residue  275 VAL
Chi-restraints excluded: chain I residue  325 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 18 optimal weight:    0.3980
   chunk 12 optimal weight:    9.9990
   chunk 58 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 296 ASN
** A 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 296 ASN
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 GLN
** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 296 ASN
** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 296 ASN
** D 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 296 ASN
** E 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
F 296 ASN
** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 296 ASN
** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 296 ASN
I 296 ASN
** I 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
J 296 ASN
** J 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4967 r_free = 0.4967 target = 0.223876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4562 r_free = 0.4562 target = 0.177791 restraints weight = 34630.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.4595 rms_B_bonded: 5.94
r_work: 0.4336 rms_B_bonded: 5.63 restraints_weight: 2.0000
r_work (final): 0.4336
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4338
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4338 r_free = 0.4338    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4339 r_free = 0.4339    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4339
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.3823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6480  Z= 0.113
  Angle     :  0.569   5.723   8670  Z= 0.298
  Chirality :  0.050   0.194    950
  Planarity :  0.004   0.036   1130
  Dihedral  :  5.356  27.549    871
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  6.47 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 23.15 %
    Favored  : 71.64 %
  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: -3.32 (0.26), residues: 850
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.52 (0.20), residues: 850

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.002   TYR C 310 
 HIS   0.001   0.000   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6470)
  covalent geometry    : angle       0.56925 ( 8650)
  SS BOND              : bond        0.00140 (   10)
  SS BOND              : angle       0.47501 (   20)
  hydrogen bonds       : bond        0.02009 (  149)
  hydrogen bonds       : angle       5.49409 (  447)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 142
  time to evaluate  : 0.198 
Fit side-chains
REVERT: B  290 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8042 (tttm)
REVERT: D  280 LYS cc_start: 0.9302 (tttt) cc_final: 0.9046 (tttt)
REVERT: F  320 SER cc_start: 0.9102 (m) cc_final: 0.8667 (p)
REVERT: H  290 LYS cc_start: 0.8544 (ttpt) cc_final: 0.7765 (ttpt)
REVERT: I  296 ASN cc_start: 0.8305 (m110) cc_final: 0.7359 (p0)
REVERT: I  298 LYS cc_start: 0.8735 (mttm) cc_final: 0.7423 (mmtt)
REVERT: I  311 LYS cc_start: 0.8113 (mttt) cc_final: 0.7075 (mmtt)
REVERT: J  296 ASN cc_start: 0.8020 (m110) cc_final: 0.7161 (p0)
REVERT: J  298 LYS cc_start: 0.8468 (mttm) cc_final: 0.8152 (mtpp)
  outliers start: 13
  outliers final: 11
  residues processed: 147
  average time/residue: 0.0803
  time to fit residues: 15.8074
Evaluate side-chains
  149 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 138
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 GLN
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  288 GLN
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain G residue  275 VAL
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain I residue  275 VAL
Chi-restraints excluded: chain I residue  325 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 68 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 46 optimal weight:    2.9990
   chunk 41 optimal weight:    8.9990
   chunk 65 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 296 ASN
A 307 GLN
** A 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 296 ASN
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 GLN
** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 296 ASN
** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 296 ASN
** D 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 296 ASN
** E 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
F 296 ASN
G 296 ASN
** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 296 ASN
I 296 ASN
** I 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
J 296 ASN
** J 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4921 r_free = 0.4921 target = 0.219566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.173431 restraints weight = 34124.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.4539 rms_B_bonded: 6.05
r_work: 0.4270 rms_B_bonded: 5.56 restraints_weight: 2.0000
r_work (final): 0.4270
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4278
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4278 r_free = 0.4278    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4278 r_free = 0.4278    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4278
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.3750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   6480  Z= 0.153
  Angle     :  0.592   6.817   8670  Z= 0.309
  Chirality :  0.050   0.188    950
  Planarity :  0.004   0.035   1130
  Dihedral  :  5.356  27.096    871
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  1.03 %
    Allowed  :  7.50 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 22.88 %
    Favored  : 71.78 %
  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 (0.26), residues: 850
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.51 (0.20), residues: 850

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.002   TYR C 310 
 HIS   0.002   0.000   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 6470)
  covalent geometry    : angle       0.59199 ( 8650)
  SS BOND              : bond        0.00241 (   10)
  SS BOND              : angle       0.58106 (   20)
  hydrogen bonds       : bond        0.02265 (  149)
  hydrogen bonds       : angle       5.55117 (  447)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 144
  time to evaluate  : 0.199 
Fit side-chains
REVERT: B  290 LYS cc_start: 0.8536 (ttmt) cc_final: 0.7992 (tttm)
REVERT: F  290 LYS cc_start: 0.8619 (ttpt) cc_final: 0.7398 (ttpt)
REVERT: F  311 LYS cc_start: 0.8527 (mttt) cc_final: 0.7173 (pttm)
REVERT: F  320 SER cc_start: 0.9074 (m) cc_final: 0.8602 (p)
REVERT: H  290 LYS cc_start: 0.8593 (ttpt) cc_final: 0.7775 (ttpt)
REVERT: I  296 ASN cc_start: 0.7985 (m-40) cc_final: 0.7178 (p0)
REVERT: I  298 LYS cc_start: 0.8744 (mttm) cc_final: 0.7485 (mmtt)
REVERT: I  311 LYS cc_start: 0.8209 (mttt) cc_final: 0.7148 (mmtt)
REVERT: J  296 ASN cc_start: 0.7583 (m-40) cc_final: 0.6942 (p0)
REVERT: J  298 LYS cc_start: 0.8507 (mttm) cc_final: 0.8173 (mtpp)
REVERT: J  311 LYS cc_start: 0.8161 (mttt) cc_final: 0.7275 (mmtt)
  outliers start: 14
  outliers final: 12
  residues processed: 149
  average time/residue: 0.0776
  time to fit residues: 15.3033
Evaluate side-chains
  154 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 142
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  288 GLN
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  288 GLN
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain G residue  275 VAL
Chi-restraints excluded: chain G residue  320 SER
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain I residue  275 VAL
Chi-restraints excluded: chain I residue  325 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 12 optimal weight:   10.0000
   chunk 59 optimal weight:    0.5980
   chunk 65 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 61 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 296 ASN
A 307 GLN
** A 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 296 ASN
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 GLN
** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 296 ASN
** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 296 ASN
** D 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 296 ASN
** E 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
F 296 ASN
** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 296 ASN
** G 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 296 ASN
I 296 ASN
** I 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
J 296 ASN
** J 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 329 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4959 r_free = 0.4959 target = 0.221977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4559 r_free = 0.4559 target = 0.175584 restraints weight = 34265.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.4617 rms_B_bonded: 6.30
r_work: 0.4306 rms_B_bonded: 6.07 restraints_weight: 2.0000
r_work (final): 0.4306
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4271
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4271 r_free = 0.4271    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4271 r_free = 0.4271    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4271
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.4007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6480  Z= 0.110
  Angle     :  0.566   6.590   8670  Z= 0.295
  Chirality :  0.050   0.171    950
  Planarity :  0.004   0.037   1130
  Dihedral  :  5.225  26.748    871
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  1.03 %
    Allowed  :  6.76 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 22.74 %
    Favored  : 72.19 %
  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: -3.23 (0.26), residues: 850
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.45 (0.20), residues: 850

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.012   0.002   TYR C 310 
 HIS   0.001   0.000   HIS I 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 6470)
  covalent geometry    : angle       0.56589 ( 8650)
  SS BOND              : bond        0.00159 (   10)
  SS BOND              : angle       0.46941 (   20)
  hydrogen bonds       : bond        0.01956 (  149)
  hydrogen bonds       : angle       5.38122 (  447)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1780.35 seconds
wall clock time: 31 minutes 53.68 seconds (1913.68 seconds total)