Starting phenix.real_space_refine
on Sat Jan 20 06:06:47 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjv_14023/01_2024/7qjv_14023.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjv_14023/01_2024/7qjv_14023.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjv_14023/01_2024/7qjv_14023.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjv_14023/01_2024/7qjv_14023.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjv_14023/01_2024/7qjv_14023.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjv_14023/01_2024/7qjv_14023.pdb"
  }
  resolution = 3.29
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.003 sd=   0.009
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      12      5.16       5
     C    4272      2.51       5
     N    1236      2.21       5
     O    1284      1.98       5
     H    7056      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  342": "OE1" <-> "OE2"
    Residue "F GLU  342": "OE1" <-> "OE2"
    Residue "B GLU  342": "OE1" <-> "OE2"
    Residue "C GLU  342": "OE1" <-> "OE2"
    Residue "D GLU  342": "OE1" <-> "OE2"
    Residue "E GLU  342": "OE1" <-> "OE2"
    Residue "K GLU  342": "OE1" <-> "OE2"
    Residue "G GLU  342": "OE1" <-> "OE2"
    Residue "H GLU  342": "OE1" <-> "OE2"
    Residue "I GLU  342": "OE1" <-> "OE2"
    Residue "J GLU  342": "OE1" <-> "OE2"
    Residue "L GLU  342": "OE1" <-> "OE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib"
  Total number of atoms: 13860
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 1155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1155
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "F"
      Number of atoms: 1155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1155
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "B"
      Number of atoms: 1155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1155
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "C"
      Number of atoms: 1155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1155
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "D"
      Number of atoms: 1155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1155
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "E"
      Number of atoms: 1155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1155
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "K"
      Number of atoms: 1155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1155
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "G"
      Number of atoms: 1155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1155
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "H"
      Number of atoms: 1155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1155
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "I"
      Number of atoms: 1155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1155
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "J"
      Number of atoms: 1155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1155
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "L"
      Number of atoms: 1155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1155
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
  Time building chain proxies: 6.48, per 1000 atoms: 0.47
  Number of scatterers: 13860
  At special positions: 0
  Unit cell: (145.024, 171.392, 41.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      12     16.00
     O    1284      8.00
     N    1236      7.00
     C    4272      6.00
     H    7056      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 12.11
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1560

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 33 sheets defined
      0.0% alpha, 50.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.36
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310
      removed outlier: 6.534A  pdb=" N   GLN A 307 " --> pdb=" O   ILE D 308 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   TYR D 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   VAL A 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314
      removed outlier: 6.611A  pdb=" N   VAL A 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 322
      removed outlier: 6.569A  pdb=" N   LYS A 317 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   SER D 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   THR A 319 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
      removed outlier: 8.399A  pdb=" N   CYS D 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   LYS A 321 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 330
      removed outlier: 6.977A  pdb=" N   GLY D 326 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ASN A 327 " --> pdb=" O   GLY D 326 " (cutoff:3.500A)
      removed outlier: 6.006A  pdb=" N   GLY B 326 " --> pdb=" O   ASN D 327 " (cutoff:3.500A)
      removed outlier: 8.543A  pdb=" N   HIS D 329 " --> pdb=" O   GLY B 326 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ILE B 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340
      removed outlier: 6.429A  pdb=" N   GLN A 336 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 8.275A  pdb=" N   VAL D 339 " --> pdb=" O   GLN A 336 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   GLU A 338 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 346
      removed outlier: 6.313A  pdb=" N   LYS A 343 " --> pdb=" O   LEU D 344 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   PHE D 346 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ASP A 345 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 354
      removed outlier: 6.573A  pdb=" N   GLN A 351 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 8.101A  pdb=" N   ILE D 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   LYS A 353 " --> pdb=" O   ILE D 354 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362
      removed outlier: 6.690A  pdb=" N   ASN B 359 " --> pdb=" O   ILE D 360 " (cutoff:3.500A)
      removed outlier: 8.203A  pdb=" N   HIS D 362 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   THR B 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 377
      removed outlier: 6.552A  pdb=" N   LYS A 369 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 8.098A  pdb=" N   GLU D 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ILE A 371 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 8.021A  pdb=" N   HIS D 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   THR A 373 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
      removed outlier: 7.961A  pdb=" N   LEU D 376 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   LYS A 375 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   LYS B 370 " --> pdb=" O   ILE D 371 " (cutoff:3.500A)
      removed outlier: 8.402A  pdb=" N   THR D 373 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   GLU B 372 " --> pdb=" O   THR D 373 " (cutoff:3.500A)
      removed outlier: 8.493A  pdb=" N   LYS D 375 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   HIS B 374 " --> pdb=" O   LYS D 375 " (cutoff:3.500A)
      removed outlier: 8.256A  pdb=" N   THR D 377 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   LEU B 376 " --> pdb=" O   THR D 377 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'F' and resid 306 through 310
    Processing sheet with id=AB2, first strand: chain 'F' and resid 313 through 322
      removed outlier: 6.452A  pdb=" N   VAL F 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   SER E 316 " --> pdb=" O   VAL F 313 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LEU F 315 " --> pdb=" O   SER E 316 " (cutoff:3.500A)
      removed outlier: 8.432A  pdb=" N   VAL E 318 " --> pdb=" O   LEU F 315 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   LYS F 317 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
      removed outlier: 7.837A  pdb=" N   SER E 320 " --> pdb=" O   LYS F 317 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   THR F 319 " --> pdb=" O   SER E 320 " (cutoff:3.500A)
      removed outlier: 8.407A  pdb=" N   CYS E 322 " --> pdb=" O   THR F 319 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   LYS F 321 " --> pdb=" O   CYS E 322 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   ASP C 314 " --> pdb=" O   LEU E 315 " (cutoff:3.500A)
      removed outlier: 7.524A  pdb=" N   LYS E 317 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   SER C 316 " --> pdb=" O   LYS E 317 " (cutoff:3.500A)
      removed outlier: 7.874A  pdb=" N   THR E 319 " --> pdb=" O   SER C 316 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   VAL C 318 " --> pdb=" O   THR E 319 " (cutoff:3.500A)
      removed outlier: 8.178A  pdb=" N   LYS E 321 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   SER C 320 " --> pdb=" O   LYS E 321 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'F' and resid 325 through 330
      removed outlier: 7.027A  pdb=" N   GLY E 326 " --> pdb=" O   LEU F 325 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   ASN F 327 " --> pdb=" O   GLY E 326 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   GLY C 326 " --> pdb=" O   LEU E 325 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ASN E 327 " --> pdb=" O   GLY C 326 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 336 through 340
    Processing sheet with id=AB5, first strand: chain 'F' and resid 343 through 346
      removed outlier: 5.913A  pdb=" N   LYS F 343 " --> pdb=" O   LEU E 344 " (cutoff:3.500A)
      removed outlier: 7.319A  pdb=" N   PHE E 346 " --> pdb=" O   LYS F 343 " (cutoff:3.500A)
      removed outlier: 6.079A  pdb=" N   ASP F 345 " --> pdb=" O   PHE E 346 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 351 through 354
      removed outlier: 6.583A  pdb=" N   GLN F 351 " --> pdb=" O   SER E 352 " (cutoff:3.500A)
      removed outlier: 8.117A  pdb=" N   ILE E 354 " --> pdb=" O   GLN F 351 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   LYS F 353 " --> pdb=" O   ILE E 354 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 359 through 362
      removed outlier: 6.670A  pdb=" N   ASN C 359 " --> pdb=" O   ILE E 360 " (cutoff:3.500A)
      removed outlier: 8.249A  pdb=" N   HIS E 362 " --> pdb=" O   ASN C 359 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   THR C 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 370 through 373
      removed outlier: 6.526A  pdb=" N   ILE F 371 " --> pdb=" O   GLU E 372 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 376 through 377
      removed outlier: 6.620A  pdb=" N   LEU C 376 " --> pdb=" O   THR E 377 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'K' and resid 306 through 310
      removed outlier: 6.423A  pdb=" N   GLN K 307 " --> pdb=" O   ILE J 308 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   TYR J 310 " --> pdb=" O   GLN K 307 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   VAL K 309 " --> pdb=" O   TYR J 310 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'K' and resid 313 through 322
      removed outlier: 6.047A  pdb=" N   ASP H 314 " --> pdb=" O   LEU J 315 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   LYS J 317 " --> pdb=" O   ASP H 314 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   SER H 316 " --> pdb=" O   LYS J 317 " (cutoff:3.500A)
      removed outlier: 7.965A  pdb=" N   THR J 319 " --> pdb=" O   SER H 316 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   VAL H 318 " --> pdb=" O   THR J 319 " (cutoff:3.500A)
      removed outlier: 8.181A  pdb=" N   LYS J 321 " --> pdb=" O   VAL H 318 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   SER H 320 " --> pdb=" O   LYS J 321 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'K' and resid 325 through 330
      removed outlier: 6.968A  pdb=" N   GLY J 326 " --> pdb=" O   LEU K 325 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   ASN K 327 " --> pdb=" O   GLY J 326 " (cutoff:3.500A)
      removed outlier: 5.769A  pdb=" N   GLY H 326 " --> pdb=" O   ASN J 327 " (cutoff:3.500A)
      removed outlier: 8.283A  pdb=" N   HIS J 329 " --> pdb=" O   GLY H 326 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   ILE H 328 " --> pdb=" O   HIS J 329 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'K' and resid 336 through 340
      removed outlier: 6.640A  pdb=" N   GLN K 336 " --> pdb=" O   VAL J 337 " (cutoff:3.500A)
      removed outlier: 8.420A  pdb=" N   VAL J 339 " --> pdb=" O   GLN K 336 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   GLU K 338 " --> pdb=" O   VAL J 339 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'K' and resid 343 through 346
      removed outlier: 6.325A  pdb=" N   LYS K 343 " --> pdb=" O   LEU J 344 " (cutoff:3.500A)
      removed outlier: 7.813A  pdb=" N   PHE J 346 " --> pdb=" O   LYS K 343 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   ASP K 345 " --> pdb=" O   PHE J 346 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'K' and resid 351 through 354
      removed outlier: 6.456A  pdb=" N   GLN K 351 " --> pdb=" O   SER J 352 " (cutoff:3.500A)
      removed outlier: 7.880A  pdb=" N   ILE J 354 " --> pdb=" O   GLN K 351 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   LYS K 353 " --> pdb=" O   ILE J 354 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'K' and resid 359 through 362
      removed outlier: 6.676A  pdb=" N   ASN H 359 " --> pdb=" O   ILE J 360 " (cutoff:3.500A)
      removed outlier: 8.122A  pdb=" N   HIS J 362 " --> pdb=" O   ASN H 359 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   THR H 361 " --> pdb=" O   HIS J 362 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'K' and resid 369 through 377
    Processing sheet with id=AC9, first strand: chain 'G' and resid 306 through 310
      removed outlier: 6.464A  pdb=" N   VAL I 306 " --> pdb=" O   GLN L 307 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   VAL L 309 " --> pdb=" O   VAL I 306 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ILE I 308 " --> pdb=" O   VAL L 309 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'G' and resid 313 through 322
      removed outlier: 6.599A  pdb=" N   VAL G 313 " --> pdb=" O   ASP L 314 " (cutoff:3.500A)
      removed outlier: 8.002A  pdb=" N   SER L 316 " --> pdb=" O   VAL G 313 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   LEU G 315 " --> pdb=" O   SER L 316 " (cutoff:3.500A)
      removed outlier: 8.397A  pdb=" N   VAL L 318 " --> pdb=" O   LEU G 315 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   LYS G 317 " --> pdb=" O   VAL L 318 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   SER L 320 " --> pdb=" O   LYS G 317 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   THR G 319 " --> pdb=" O   SER L 320 " (cutoff:3.500A)
      removed outlier: 8.328A  pdb=" N   CYS L 322 " --> pdb=" O   THR G 319 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   LYS G 321 " --> pdb=" O   CYS L 322 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   ASP I 314 " --> pdb=" O   LEU L 315 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   LYS L 317 " --> pdb=" O   ASP I 314 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   SER I 316 " --> pdb=" O   LYS L 317 " (cutoff:3.500A)
      removed outlier: 7.803A  pdb=" N   THR L 319 " --> pdb=" O   SER I 316 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   VAL I 318 " --> pdb=" O   THR L 319 " (cutoff:3.500A)
      removed outlier: 8.232A  pdb=" N   LYS L 321 " --> pdb=" O   VAL I 318 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   SER I 320 " --> pdb=" O   LYS L 321 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD1
    Processing sheet with id=AD2, first strand: chain 'G' and resid 325 through 330
      removed outlier: 8.849A  pdb=" N   LEU G 325 " --> pdb=" O   GLY L 326 " (cutoff:3.500A)
      removed outlier: 9.760A  pdb=" N   ILE L 328 " --> pdb=" O   LEU G 325 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   ASN G 327 " --> pdb=" O   ILE L 328 " (cutoff:3.500A)
      removed outlier: 8.157A  pdb=" N   HIS L 330 " --> pdb=" O   ASN G 327 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   HIS G 329 " --> pdb=" O   HIS L 330 " (cutoff:3.500A)
      removed outlier: 5.897A  pdb=" N   GLY I 326 " --> pdb=" O   ASN L 327 " (cutoff:3.500A)
      removed outlier: 8.368A  pdb=" N   HIS L 329 " --> pdb=" O   GLY I 326 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   ILE I 328 " --> pdb=" O   HIS L 329 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD2
    Processing sheet with id=AD3, first strand: chain 'G' and resid 336 through 346
      removed outlier: 6.834A  pdb=" N   VAL G 337 " --> pdb=" O   GLN L 336 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   GLU L 338 " --> pdb=" O   VAL G 337 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   VAL G 339 " --> pdb=" O   GLU L 338 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   LYS L 340 " --> pdb=" O   VAL G 339 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   SER G 341 " --> pdb=" O   LYS L 340 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   GLU L 342 " --> pdb=" O   SER G 341 " (cutoff:3.500A)
      removed outlier: 8.921A  pdb=" N   GLN I 336 " --> pdb=" O   VAL L 337 " (cutoff:3.500A)
      removed outlier: 10.397A  pdb=" N   VAL L 339 " --> pdb=" O   GLN I 336 " (cutoff:3.500A)
      removed outlier: 8.898A  pdb=" N   GLU I 338 " --> pdb=" O   VAL L 339 " (cutoff:3.500A)
      removed outlier: 10.292A  pdb=" N   SER L 341 " --> pdb=" O   GLU I 338 " (cutoff:3.500A)
      removed outlier: 9.012A  pdb=" N   LYS I 340 " --> pdb=" O   SER L 341 " (cutoff:3.500A)
      removed outlier: 9.024A  pdb=" N   LYS L 343 " --> pdb=" O   LYS I 340 " (cutoff:3.500A)
      removed outlier: 5.162A  pdb=" N   GLU I 342 " --> pdb=" O   LYS L 343 " (cutoff:3.500A)
      removed outlier: 7.426A  pdb=" N   ASP L 345 " --> pdb=" O   GLU I 342 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   LEU I 344 " --> pdb=" O   ASP L 345 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'G' and resid 351 through 354
      removed outlier: 6.484A  pdb=" N   GLN G 351 " --> pdb=" O   SER L 352 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   ILE L 354 " --> pdb=" O   GLN G 351 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   LYS G 353 " --> pdb=" O   ILE L 354 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'G' and resid 359 through 362
      removed outlier: 6.653A  pdb=" N   ASN I 359 " --> pdb=" O   ILE L 360 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   HIS L 362 " --> pdb=" O   ASN I 359 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   THR I 361 " --> pdb=" O   HIS L 362 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'G' and resid 369 through 377

    136 hydrogen bonds defined for protein.
    408 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: 4.59

  Time building geometry restraints manager: 12.21 seconds

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

  Histogram of bond lengths:
        0.94 -     1.12: 7044
        1.12 -     1.29: 1154
        1.29 -     1.47: 2358
        1.47 -     1.64: 3400
        1.64 -     1.82: 12
  Bond restraints: 13968
  Sorted by residual:
  bond pdb=" ND1 HIS E 330 "
       pdb=" HD1 HIS E 330 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.73e+01
  bond pdb=" CD1 PHE K 346 "
       pdb=" HD1 PHE K 346 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" N   GLN B 351 "
       pdb=" H   GLN B 351 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" N   ILE B 354 "
       pdb=" H   ILE B 354 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" N   LEU B 357 "
       pdb=" H   LEU B 357 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  ... (remaining 13963 not shown)

  Histogram of bond angle deviations from ideal:
       94.51 -   102.14: 39
      102.14 -   109.77: 11647
      109.77 -   117.40: 7319
      117.40 -   125.02: 6013
      125.02 -   132.65: 446
  Bond angle restraints: 25464
  Sorted by residual:
  angle pdb=" C   SER F 305 "
        pdb=" N   VAL F 306 "
        pdb=" CA  VAL F 306 "
      ideal   model   delta    sigma   weight residual
     123.10  132.65   -9.55 1.29e+00 6.01e-01 5.48e+01
  angle pdb=" CA  VAL F 306 "
        pdb=" C   VAL F 306 "
        pdb=" N   GLN F 307 "
      ideal   model   delta    sigma   weight residual
     116.10  124.74   -8.64 1.25e+00 6.40e-01 4.78e+01
  angle pdb=" N   ASP A 358 "
        pdb=" CA  ASP A 358 "
        pdb=" C   ASP A 358 "
      ideal   model   delta    sigma   weight residual
     109.46  120.73  -11.27 1.66e+00 3.63e-01 4.61e+01
  angle pdb=" N   GLY I 335 "
        pdb=" CA  GLY I 335 "
        pdb=" C   GLY I 335 "
      ideal   model   delta    sigma   weight residual
     110.96  118.71   -7.75 1.19e+00 7.06e-01 4.24e+01
  angle pdb=" N   VAL F 306 "
        pdb=" CA  VAL F 306 "
        pdb=" C   VAL F 306 "
      ideal   model   delta    sigma   weight residual
     108.53  117.98   -9.45 1.45e+00 4.76e-01 4.24e+01
  ... (remaining 25459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.48: 5475
       14.48 -    28.95: 457
       28.95 -    43.43: 84
       43.43 -    57.91: 90
       57.91 -    72.38: 98
  Dihedral angle restraints: 6204
    sinusoidal: 3432
      harmonic: 2772
  Sorted by residual:
  dihedral pdb=" C   HIS E 374 "
           pdb=" N   HIS E 374 "
           pdb=" CA  HIS E 374 "
           pdb=" CB  HIS E 374 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -142.65   20.05     0      2.50e+00 1.60e-01 6.43e+01
  dihedral pdb=" N   HIS E 374 "
           pdb=" C   HIS E 374 "
           pdb=" CA  HIS E 374 "
           pdb=" CB  HIS E 374 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  140.34  -17.54     0      2.50e+00 1.60e-01 4.92e+01
  dihedral pdb=" C   THR E 373 "
           pdb=" N   THR E 373 "
           pdb=" CA  THR E 373 "
           pdb=" CB  THR E 373 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -138.97   16.97     0      2.50e+00 1.60e-01 4.61e+01
  ... (remaining 6201 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.162: 938
       0.162 -    0.323: 98
       0.323 -    0.485: 6
       0.485 -    0.646: 1
       0.646 -    0.808: 1
  Chirality restraints: 1044
  Sorted by residual:
  chirality pdb=" CA  HIS E 374 "
            pdb=" N   HIS E 374 "
            pdb=" C   HIS E 374 "
            pdb=" CB  HIS E 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.70    0.81 2.00e-01 2.50e+01 1.63e+01
  chirality pdb=" CA  THR E 373 "
            pdb=" N   THR E 373 "
            pdb=" C   THR E 373 "
            pdb=" CB  THR E 373 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.94    0.59 2.00e-01 2.50e+01 8.65e+00
  chirality pdb=" CA  LYS K 343 "
            pdb=" N   LYS K 343 "
            pdb=" C   LYS K 343 "
            pdb=" CB  LYS K 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.42e+00
  ... (remaining 1041 not shown)

  Planarity restraints: 2028
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR K 310 "   -0.151 2.00e-02 2.50e+03   6.18e-02 1.15e+02
        pdb=" CG  TYR K 310 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TYR K 310 "    0.052 2.00e-02 2.50e+03
        pdb=" CD2 TYR K 310 "    0.053 2.00e-02 2.50e+03
        pdb=" CE1 TYR K 310 "    0.043 2.00e-02 2.50e+03
        pdb=" CE2 TYR K 310 "    0.022 2.00e-02 2.50e+03
        pdb=" CZ  TYR K 310 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR K 310 "   -0.108 2.00e-02 2.50e+03
        pdb=" HD1 TYR K 310 "    0.007 2.00e-02 2.50e+03
        pdb=" HD2 TYR K 310 "    0.042 2.00e-02 2.50e+03
        pdb=" HE1 TYR K 310 "    0.009 2.00e-02 2.50e+03
        pdb=" HE2 TYR K 310 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR J 310 "   -0.135 2.00e-02 2.50e+03   5.88e-02 1.04e+02
        pdb=" CG  TYR J 310 "    0.022 2.00e-02 2.50e+03
        pdb=" CD1 TYR J 310 "    0.052 2.00e-02 2.50e+03
        pdb=" CD2 TYR J 310 "    0.046 2.00e-02 2.50e+03
        pdb=" CE1 TYR J 310 "    0.049 2.00e-02 2.50e+03
        pdb=" CE2 TYR J 310 "    0.023 2.00e-02 2.50e+03
        pdb=" CZ  TYR J 310 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR J 310 "   -0.114 2.00e-02 2.50e+03
        pdb=" HD1 TYR J 310 "    0.001 2.00e-02 2.50e+03
        pdb=" HD2 TYR J 310 "    0.040 2.00e-02 2.50e+03
        pdb=" HE1 TYR J 310 "    0.018 2.00e-02 2.50e+03
        pdb=" HE2 TYR J 310 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 310 "    0.134 2.00e-02 2.50e+03   5.28e-02 8.36e+01
        pdb=" CG  TYR F 310 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 310 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 310 "   -0.042 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 310 "   -0.026 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 310 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 310 "    0.007 2.00e-02 2.50e+03
        pdb=" OH  TYR F 310 "    0.085 2.00e-02 2.50e+03
        pdb=" HD1 TYR F 310 "   -0.014 2.00e-02 2.50e+03
        pdb=" HD2 TYR F 310 "   -0.035 2.00e-02 2.50e+03
        pdb=" HE1 TYR F 310 "   -0.005 2.00e-02 2.50e+03
        pdb=" HE2 TYR F 310 "    0.003 2.00e-02 2.50e+03
  ... (remaining 2025 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 906
        2.15 -     2.76: 23801
        2.76 -     3.38: 36640
        3.38 -     3.99: 49445
        3.99 -     4.60: 71410
  Nonbonded interactions: 182202
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" HG  SER E 316 "
     model   vdw
     1.540 1.850
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" HG  SER A 316 "
     model   vdw
     1.544 1.850
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" HG  SER F 316 "
     model   vdw
     1.544 1.850
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" HG  SER D 316 "
     model   vdw
     1.557 1.850
  nonbonded pdb=" OD1 ASP G 314 "
            pdb=" HG  SER G 316 "
     model   vdw
     1.563 1.850
  ... (remaining 182197 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
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'
  selection = chain 'K'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.140
  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:             0.140
  Extract box with map and model:          3.750
  Check model and map are aligned:         0.000
  Set scattering table:                    0.050
  Process input model:                     46.750
  Find NCS groups from input model:        0.590
  Set up NCS constraints:                  0.070
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   55.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
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      :  0.012   0.087   6912  Z= 0.816
  Angle     :  2.133  11.266   9252  Z= 1.385
  Chirality :  0.107   0.808   1044
  Planarity :  0.013   0.103   1176
  Dihedral  : 11.772  69.750   2628
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 0.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.15 %
    Favored  : 98.72 %
  Cbeta Deviations :  0.90 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.07 (0.20), residues: 876
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.57 (0.16), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.021   0.006   HIS G 362 
 PHE   0.039   0.012   PHE H 378 
 TYR   0.137   0.038   TYR K 310 
 ARG   0.006   0.001   ARG C 349 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  9 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 8
  time to evaluate  : 1.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 9
  average time/residue: 0.3105
  time to fit residues: 6.2312
Evaluate side-chains
  3 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 1.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    6.9990
   chunk 63 optimal weight:    6.9990
   chunk 35 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 42 optimal weight:    5.9990
   chunk 34 optimal weight:    8.9990
   chunk 65 optimal weight:    8.9990
   chunk 25 optimal weight:    6.9990
   chunk 40 optimal weight:    8.9990
   chunk 49 optimal weight:    6.9990
   chunk 76 optimal weight:    6.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
F 362 HIS
C 368 ASN
E 374 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6912  Z= 0.231
  Angle     :  0.603   6.661   9252  Z= 0.332
  Chirality :  0.052   0.132   1044
  Planarity :  0.005   0.066   1176
  Dihedral  :  6.855  22.958    912
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  1.54 %
    Favored  : 98.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.21), residues: 876
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.55 (0.16), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.002   HIS E 374 
 PHE   0.010   0.001   PHE L 346 
 TYR   0.012   0.002   TYR L 310 
 ARG   0.005   0.002   ARG A 349 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  6 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 4
  time to evaluate  : 1.126 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 6
  average time/residue: 0.2693
  time to fit residues: 4.0383
Evaluate side-chains
  2 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 1
  time to evaluate  : 1.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  342 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:   20.0000
   chunk 23 optimal weight:   20.0000
   chunk 63 optimal weight:   30.0000
   chunk 51 optimal weight:   20.0000
   chunk 21 optimal weight:   20.0000
   chunk 76 optimal weight:   20.0000
   chunk 82 optimal weight:   20.0000
   chunk 68 optimal weight:    7.9990
   chunk 75 optimal weight:    9.9990
   chunk 26 optimal weight:   20.0000
   chunk 61 optimal weight:    7.9990
   overall best weight:   13.1994

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

Flipped N/Q/H residues before XYZ refinement:
F 362 HIS
B 329 HIS
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 368 ASN
J 368 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   6912  Z= 0.367
  Angle     :  0.629   6.737   9252  Z= 0.348
  Chirality :  0.052   0.130   1044
  Planarity :  0.005   0.082   1176
  Dihedral  :  6.327  22.026    912
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.93 (0.22), residues: 876
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.47 (0.17), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.003   HIS E 362 
 PHE   0.008   0.001   PHE H 378 
 TYR   0.020   0.003   TYR G 310 
 ARG   0.003   0.001   ARG L 349 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  2 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 2
  time to evaluate  : 1.173 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 2
  average time/residue: 0.2165
  time to fit residues: 2.4532
Evaluate side-chains
  0 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 0
  time to evaluate  : 1.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:   20.0000
   chunk 57 optimal weight:    0.0570
   chunk 39 optimal weight:   20.0000
   chunk 8 optimal weight:    6.9990
   chunk 36 optimal weight:    5.9990
   chunk 51 optimal weight:    9.9990
   chunk 76 optimal weight:    9.9990
   chunk 81 optimal weight:   20.0000
   chunk 40 optimal weight:   20.0000
   chunk 72 optimal weight:   10.0000
   chunk 21 optimal weight:   20.0000
   overall best weight:    6.6106

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 374 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   6912  Z= 0.187
  Angle     :  0.500   4.533   9252  Z= 0.272
  Chirality :  0.050   0.133   1044
  Planarity :  0.004   0.079   1176
  Dihedral  :  5.830  20.788    912
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  4.49 %
    Favored  : 95.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.22), residues: 876
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.39 (0.17), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 362 
 PHE   0.006   0.001   PHE F 346 
 TYR   0.007   0.001   TYR F 310 
 ARG   0.001   0.000   ARG B 349 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  5 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 2
  time to evaluate  : 1.247 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 5
  average time/residue: 0.2255
  time to fit residues: 3.5707
Evaluate side-chains
  2 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 1
  time to evaluate  : 1.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  342 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 46 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   chunk 33 optimal weight:   20.0000
   chunk 69 optimal weight:    5.9990
   chunk 56 optimal weight:   20.0000
   chunk 0 optimal weight:   30.0000
   chunk 41 optimal weight:   20.0000
   chunk 72 optimal weight:   20.0000
   chunk 20 optimal weight:    1.9990
   overall best weight:    5.9992

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.3436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6912  Z= 0.187
  Angle     :  0.473   3.843   9252  Z= 0.257
  Chirality :  0.050   0.131   1044
  Planarity :  0.004   0.071   1176
  Dihedral  :  5.428  20.333    912
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  5.00 %
    Favored  : 94.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.71 (0.23), residues: 876
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.29 (0.18), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS E 362 
 PHE   0.004   0.001   PHE F 346 
 TYR   0.009   0.002   TYR G 310 
 ARG   0.002   0.000   ARG C 349 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  4 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 1
  time to evaluate  : 1.241 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 4
  average time/residue: 0.2051
  time to fit residues: 3.0430
Evaluate side-chains
  2 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 1
  time to evaluate  : 1.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  358 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 73 optimal weight:   20.0000
   chunk 16 optimal weight:   10.0000
   chunk 47 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 81 optimal weight:   20.0000
   chunk 67 optimal weight:    9.9990
   chunk 37 optimal weight:   10.0000
   chunk 6 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 42 optimal weight:   20.0000
   overall best weight:    8.1992

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.3710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6912  Z= 0.228
  Angle     :  0.494   4.883   9252  Z= 0.268
  Chirality :  0.050   0.132   1044
  Planarity :  0.004   0.073   1176
  Dihedral  :  5.482  21.484    912
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  5.38 %
    Favored  : 94.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.23), residues: 876
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.37 (0.18), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS E 362 
 PHE   0.004   0.001   PHE J 378 
 TYR   0.010   0.002   TYR J 310 
 ARG   0.002   0.000   ARG C 349 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  5 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 1
  time to evaluate  : 1.225 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 5
  average time/residue: 0.2273
  time to fit residues: 3.7173
Evaluate side-chains
  4 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 1
  time to evaluate  : 1.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain E residue  358 ASP
Chi-restraints excluded: chain J residue  358 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 78 optimal weight:   20.0000
   chunk 9 optimal weight:   20.0000
   chunk 46 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 45 optimal weight:   10.0000
   chunk 68 optimal weight:   10.0000
   chunk 80 optimal weight:    8.9990
   chunk 50 optimal weight:    9.9990
   chunk 49 optimal weight:   20.0000
   chunk 37 optimal weight:   10.0000
   chunk 32 optimal weight:   20.0000
   overall best weight:    7.7992

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 368 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.3890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6912  Z= 0.214
  Angle     :  0.475   4.313   9252  Z= 0.257
  Chirality :  0.050   0.131   1044
  Planarity :  0.004   0.068   1176
  Dihedral  :  5.343  21.518    912
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  5.51 %
    Favored  : 93.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.23), residues: 876
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.35 (0.18), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E 362 
 PHE   0.004   0.001   PHE J 378 
 TYR   0.009   0.002   TYR E 310 
 ARG   0.001   0.000   ARG C 349 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  5 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 1
  time to evaluate  : 1.131 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 5
  average time/residue: 0.2139
  time to fit residues: 3.4268
Evaluate side-chains
  4 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 1
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain E residue  358 ASP
Chi-restraints excluded: chain J residue  358 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 15 optimal weight:   30.0000
   chunk 51 optimal weight:    9.9990
   chunk 55 optimal weight:    0.9990
   chunk 40 optimal weight:   30.0000
   chunk 7 optimal weight:   20.0000
   chunk 63 optimal weight:   30.0000
   chunk 73 optimal weight:   20.0000
   chunk 77 optimal weight:    8.9990
   chunk 70 optimal weight:   30.0000
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.4006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6912  Z= 0.180
  Angle     :  0.462   4.286   9252  Z= 0.249
  Chirality :  0.050   0.131   1044
  Planarity :  0.004   0.068   1176
  Dihedral  :  5.259  20.752    912
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  5.77 %
    Favored  : 93.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.23), residues: 876
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.38 (0.18), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E 362 
 PHE   0.003   0.001   PHE J 378 
 TYR   0.009   0.001   TYR E 310 
 ARG   0.001   0.000   ARG F 349 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 1
  time to evaluate  : 1.210 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 3
  average time/residue: 0.2419
  time to fit residues: 2.9676
Evaluate side-chains
  3 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 1
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain E residue  358 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:   20.0000
   chunk 77 optimal weight:   30.0000
   chunk 45 optimal weight:   10.0000
   chunk 32 optimal weight:   20.0000
   chunk 59 optimal weight:    9.9990
   chunk 23 optimal weight:   20.0000
   chunk 68 optimal weight:   10.0000
   chunk 71 optimal weight:   30.0000
   chunk 49 optimal weight:    5.9990
   chunk 79 optimal weight:   20.0000
   chunk 48 optimal weight:    9.9990
   overall best weight:    9.1994

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.4121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   6912  Z= 0.256
  Angle     :  0.490   4.535   9252  Z= 0.266
  Chirality :  0.050   0.131   1044
  Planarity :  0.004   0.071   1176
  Dihedral  :  5.329  22.495    912
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  5.77 %
    Favored  : 93.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.23), residues: 876
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.43 (0.18), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E 362 
 PHE   0.003   0.001   PHE J 378 
 TYR   0.012   0.002   TYR G 310 
 ARG   0.001   0.000   ARG C 349 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  4 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 1
  time to evaluate  : 1.245 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 4
  average time/residue: 0.2318
  time to fit residues: 3.2771
Evaluate side-chains
  3 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 1
  time to evaluate  : 1.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain J residue  358 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 37 optimal weight:   20.0000
   chunk 55 optimal weight:    0.9990
   chunk 83 optimal weight:    9.9990
   chunk 77 optimal weight:   20.0000
   chunk 66 optimal weight:    0.8980
   chunk 6 optimal weight:    0.2980
   chunk 51 optimal weight:   10.0000
   chunk 40 optimal weight:   20.0000
   chunk 52 optimal weight:    9.9990
   chunk 70 optimal weight:   30.0000
   chunk 20 optimal weight:    0.0980
   overall best weight:    2.4584

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.4162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   6912  Z= 0.114
  Angle     :  0.442   3.641   9252  Z= 0.235
  Chirality :  0.050   0.128   1044
  Planarity :  0.004   0.064   1176
  Dihedral  :  5.026  19.315    912
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  6.03 %
    Favored  : 93.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.24), residues: 876
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.35 (0.18), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS G 330 
 PHE   0.003   0.001   PHE K 346 
 TYR   0.006   0.001   TYR E 310 
 ARG   0.001   0.000   ARG F 349 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 2
  time to evaluate  : 1.288 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 3
  average time/residue: 0.2109
  time to fit residues: 2.8365
Evaluate side-chains
  2 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 1
  time to evaluate  : 1.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  358 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 61 optimal weight:   20.0000
   chunk 9 optimal weight:   20.0000
   chunk 18 optimal weight:   20.0000
   chunk 66 optimal weight:    6.9990
   chunk 27 optimal weight:   10.0000
   chunk 68 optimal weight:   10.0000
   chunk 8 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   chunk 58 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 48 optimal weight:    9.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.082520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.074069 restraints weight = 89348.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.4255 rms_B_bonded: 3.53
r_work: 0.4177 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.4177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.4221
Sorry: Reduce crashed with command 'molprobity.reduce  -quiet -trim -'.
Dumping stdin to file 'reduce_fail.pdb'.
Return code: -15
Dumping stderr: