Starting phenix.real_space_refine (version: dev)
on Wed Apr  6 11:41:03 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pko_13474/04_2022/7pko_13474.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pko_13474/04_2022/7pko_13474.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pko_13474/04_2022/7pko_13474.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pko_13474/04_2022/7pko_13474.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pko_13474/04_2022/7pko_13474.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pko_13474/04_2022/7pko_13474.pdb"
  }
  resolution = 3.9
  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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.007
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
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    Residue "A GLU    3": "OE1" <-> "OE2"
    Residue "A PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A ASP   45": "OD1" <-> "OD2"
    Residue "A PHE   72": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   77": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  104": "NH1" <-> "NH2"
    Residue "A GLU  112": "OE1" <-> "OE2"
    Residue "A ASP  123": "OD1" <-> "OD2"
    Residue "A ASP  130": "OD1" <-> "OD2"
    Residue "A GLU  145": "OE1" <-> "OE2"
    Residue "A GLU  147": "OE1" <-> "OE2"
    Residue "A PHE  164": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  187": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  193": "OE1" <-> "OE2"
    Residue "A ASP  199": "OD1" <-> "OD2"
    Residue "A GLU  204": "OE1" <-> "OE2"
    Residue "A TYR  226": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  231": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  256": "OD1" <-> "OD2"
    Residue "A PHE  257": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  306": "OD1" <-> "OD2"
    Residue "B PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP   39": "OD1" <-> "OD2"
    Residue "B ASP   41": "OD1" <-> "OD2"
    Residue "B ASP   45": "OD1" <-> "OD2"
    Residue "B PHE   57": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   72": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   77": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  104": "NH1" <-> "NH2"
    Residue "B GLU  112": "OE1" <-> "OE2"
    Residue "B ASP  123": "OD1" <-> "OD2"
    Residue "B GLU  147": "OE1" <-> "OE2"
    Residue "B GLU  156": "OE1" <-> "OE2"
    Residue "B PHE  164": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  181": "OD1" <-> "OD2"
    Residue "B ASP  194": "OD1" <-> "OD2"
    Residue "B GLU  208": "OE1" <-> "OE2"
    Residue "B TYR  226": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  231": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  257": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  306": "OD1" <-> "OD2"
    Residue "B ASP  310": "OD1" <-> "OD2"
    Residue "C GLU    3": "OE1" <-> "OE2"
    Residue "C ASP   15": "OD1" <-> "OD2"
    Residue "C PHE   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP   36": "OD1" <-> "OD2"
    Residue "C ASP   41": "OD1" <-> "OD2"
    Residue "C PHE   43": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP   45": "OD1" <-> "OD2"
    Residue "C TYR   61": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   72": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   77": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU   86": "OE1" <-> "OE2"
    Residue "C ARG  104": "NH1" <-> "NH2"
    Residue "C GLU  112": "OE1" <-> "OE2"
    Residue "C GLU  119": "OE1" <-> "OE2"
    Residue "C GLU  145": "OE1" <-> "OE2"
    Residue "C PHE  164": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  181": "OD1" <-> "OD2"
    Residue "C PHE  184": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  186": "OE1" <-> "OE2"
    Residue "C ASP  194": "OD1" <-> "OD2"
    Residue "C ASP  199": "OD1" <-> "OD2"
    Residue "C TYR  226": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  231": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  242": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  257": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  296": "OE1" <-> "OE2"
    Residue "D GLU    3": "OE1" <-> "OE2"
    Residue "D PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP   45": "OD1" <-> "OD2"
    Residue "D PHE   57": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE   72": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU   73": "OE1" <-> "OE2"
    Residue "D PHE   77": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ARG  104": "NH1" <-> "NH2"
    Residue "D GLU  112": "OE1" <-> "OE2"
    Residue "D GLU  119": "OE1" <-> "OE2"
    Residue "D GLU  153": "OE1" <-> "OE2"
    Residue "D PHE  164": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP  199": "OD1" <-> "OD2"
    Residue "D GLU  208": "OE1" <-> "OE2"
    Residue "D TYR  226": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR  231": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR  242": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP  261": "OD1" <-> "OD2"
    Residue "D ASP  310": "OD1" <-> "OD2"
    Residue "E PHE   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ASP   36": "OD1" <-> "OD2"
    Residue "E ASP   41": "OD1" <-> "OD2"
    Residue "E ASP   45": "OD1" <-> "OD2"
    Residue "E ASP   65": "OD1" <-> "OD2"
    Residue "E PHE   72": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E GLU   73": "OE1" <-> "OE2"
    Residue "E PHE   77": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG  104": "NH1" <-> "NH2"
    Residue "E ASP  123": "OD1" <-> "OD2"
    Residue "E GLU  153": "OE1" <-> "OE2"
    Residue "E PHE  164": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E GLU  186": "OE1" <-> "OE2"
    Residue "E TYR  187": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E GLU  193": "OE1" <-> "OE2"
    Residue "E ASP  194": "OD1" <-> "OD2"
    Residue "E ASP  199": "OD1" <-> "OD2"
    Residue "E PHE  216": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  226": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  231": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ASP  239": "OD1" <-> "OD2"
    Residue "E ASP  256": "OD1" <-> "OD2"
    Residue "E PHE  257": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  290": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F GLU    3": "OE1" <-> "OE2"
    Residue "F PHE   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ASP   45": "OD1" <-> "OD2"
    Residue "F PHE   72": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F GLU   73": "OE1" <-> "OE2"
    Residue "F PHE   77": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ARG  104": "NH1" <-> "NH2"
    Residue "F GLU  112": "OE1" <-> "OE2"
    Residue "F ASP  123": "OD1" <-> "OD2"
    Residue "F ASP  130": "OD1" <-> "OD2"
    Residue "F GLU  156": "OE1" <-> "OE2"
    Residue "F PHE  164": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F GLU  173": "OE1" <-> "OE2"
    Residue "F TYR  187": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F GLU  204": "OE1" <-> "OE2"
    Residue "F TYR  226": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  231": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ASP  239": "OD1" <-> "OD2"
    Residue "F ASP  256": "OD1" <-> "OD2"
    Residue "F PHE  257": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G ASP   41": "OD1" <-> "OD2"
    Residue "G ASP   45": "OD1" <-> "OD2"
    Residue "G ASP   65": "OD1" <-> "OD2"
    Residue "G PHE   72": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE   77": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G ARG  104": "NH1" <-> "NH2"
    Residue "G GLU  112": "OE1" <-> "OE2"
    Residue "G GLU  119": "OE1" <-> "OE2"
    Residue "G ASP  123": "OD1" <-> "OD2"
    Residue "G PHE  164": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G GLU  186": "OE1" <-> "OE2"
    Residue "G TYR  187": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G GLU  204": "OE1" <-> "OE2"
    Residue "G PHE  216": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR  226": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR  231": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR  242": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G ASP  256": "OD1" <-> "OD2"
    Residue "G PHE  257": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G ASP  306": "OD1" <-> "OD2"
    Residue "G GLU  311": "OE1" <-> "OE2"
    Residue "U GLU   13": "OE1" <-> "OE2"
    Residue "U PHE   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U ASP   36": "OD1" <-> "OD2"
    Residue "U ASP   41": "OD1" <-> "OD2"
    Residue "U ASP   45": "OD1" <-> "OD2"
    Residue "U PHE   57": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U TYR   61": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U PHE   72": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U PHE   77": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U GLU   86": "OE1" <-> "OE2"
    Residue "U ARG  104": "NH1" <-> "NH2"
    Residue "U GLU  112": "OE1" <-> "OE2"
    Residue "U ASP  123": "OD1" <-> "OD2"
    Residue "U ASP  130": "OD1" <-> "OD2"
    Residue "U GLU  145": "OE1" <-> "OE2"
    Residue "U PHE  164": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U ASP  181": "OD1" <-> "OD2"
    Residue "U TYR  187": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U GLU  204": "OE1" <-> "OE2"
    Residue "U PHE  216": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U TYR  226": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U TYR  231": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U ASP  256": "OD1" <-> "OD2"
    Residue "U PHE  257": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U GLU  296": "OE1" <-> "OE2"
  Time to flip residues: 0.13s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib"
  Total number of atoms: 20368
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2546
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2546
          Classifications: {'peptide': 313}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 302}
    Chain: "B"
      Number of atoms: 2546
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2546
          Classifications: {'peptide': 313}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 302}
    Chain: "C"
      Number of atoms: 2546
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2546
          Classifications: {'peptide': 313}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 302}
    Chain: "D"
      Number of atoms: 2546
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2546
          Classifications: {'peptide': 313}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 302}
    Chain: "E"
      Number of atoms: 2546
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2546
          Classifications: {'peptide': 313}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 302}
    Chain: "F"
      Number of atoms: 2546
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2546
          Classifications: {'peptide': 313}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 302}
    Chain: "G"
      Number of atoms: 2546
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2546
          Classifications: {'peptide': 313}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 302}
    Chain: "U"
      Number of atoms: 2546
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2546
          Classifications: {'peptide': 313}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 302}
  Time building chain proxies: 11.49, per 1000 atoms: 0.56
  Number of scatterers: 20368
  At special positions: 0
  Unit cell: (135.255, 135.255, 109.695, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     120     16.00
     O    3728      8.00
     N    3456      7.00
     C   13064      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        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: 8.58
  Conformation dependent library (CDL) restraints added in 2.9 seconds
  

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4848

  Finding SS restraints...
    Secondary structure from input PDB file:
      107 helices and 27 sheets defined
      46.2% alpha, 10.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 6
    Processing helix  chain 'A' and resid 23 through 32
      removed outlier: 3.759A  pdb=" N   THR A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 61
      removed outlier: 3.532A  pdb=" N   PHE A  57 " --> pdb=" O   PRO A  54 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   LYS A  59 " --> pdb=" O   GLN A  56 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   TYR A  61 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 89
      removed outlier: 4.243A  pdb=" N   THR A  78 " --> pdb=" O   THR A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 102
      removed outlier: 3.726A  pdb=" N   LEU A 102 " --> pdb=" O   VAL A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 119
      removed outlier: 3.715A  pdb=" N   LEU A 111 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLU A 119 " --> pdb=" O   VAL A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 139
    Processing helix  chain 'A' and resid 198 through 213
      removed outlier: 3.920A  pdb=" N   VAL A 202 " --> pdb=" O   SER A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 232
      No H-bonds generated for 'chain 'A' and resid 230 through 232'
    Processing helix  chain 'A' and resid 233 through 250
      removed outlier: 3.583A  pdb=" N   HIS A 237 " --> pdb=" O   SER A 233 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA A 243 " --> pdb=" O   ASP A 239 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   THR A 244 " --> pdb=" O   ARG A 240 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ASN A 248 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LYS A 250 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 279
      removed outlier: 3.689A  pdb=" N   GLY A 279 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 291
      removed outlier: 3.543A  pdb=" N   LYS A 286 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   LEU A 288 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   LEU A 289 " --> pdb=" O   CYS A 285 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   PHE A 290 " --> pdb=" O   LYS A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 311
    Processing helix  chain 'B' and resid 3 through 7
      removed outlier: 3.660A  pdb=" N   PHE B   7 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 32
    Processing helix  chain 'B' and resid 54 through 61
      removed outlier: 4.363A  pdb=" N   LYS B  59 " --> pdb=" O   GLN B  56 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   TYR B  61 " --> pdb=" O   LYS B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 91
      removed outlier: 4.255A  pdb=" N   THR B  78 " --> pdb=" O   THR B  74 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   SER B  90 " --> pdb=" O   GLU B  86 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU B  91 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 102
      removed outlier: 3.814A  pdb=" N   LEU B 102 " --> pdb=" O   VAL B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 120
      removed outlier: 3.835A  pdb=" N   LEU B 111 " --> pdb=" O   SER B 107 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ASN B 120 " --> pdb=" O   ILE B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 141
    Processing helix  chain 'B' and resid 148 through 152
    Processing helix  chain 'B' and resid 198 through 213
      removed outlier: 3.944A  pdb=" N   VAL B 202 " --> pdb=" O   SER B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 232
      No H-bonds generated for 'chain 'B' and resid 230 through 232'
    Processing helix  chain 'B' and resid 233 through 250
      removed outlier: 3.582A  pdb=" N   LYS B 250 " --> pdb=" O   LYS B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 279
      removed outlier: 3.711A  pdb=" N   GLY B 279 " --> pdb=" O   SER B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 291
      removed outlier: 3.717A  pdb=" N   LYS B 286 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   LEU B 288 " --> pdb=" O   VAL B 284 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   LEU B 289 " --> pdb=" O   CYS B 285 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   PHE B 290 " --> pdb=" O   LYS B 286 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLN B 291 " --> pdb=" O   ARG B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 303 through 311
    Processing helix  chain 'C' and resid 3 through 6
    Processing helix  chain 'C' and resid 23 through 32
      removed outlier: 3.569A  pdb=" N   THR C  32 " --> pdb=" O   LYS C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 54 through 61
      removed outlier: 3.529A  pdb=" N   PHE C  57 " --> pdb=" O   PRO C  54 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   LYS C  59 " --> pdb=" O   GLN C  56 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   TYR C  61 " --> pdb=" O   LYS C  58 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 91
      removed outlier: 4.101A  pdb=" N   THR C  78 " --> pdb=" O   THR C  74 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   SER C  90 " --> pdb=" O   GLU C  86 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU C  91 " --> pdb=" O   ALA C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 97 through 102
    Processing helix  chain 'C' and resid 107 through 119
      removed outlier: 3.683A  pdb=" N   LEU C 111 " --> pdb=" O   SER C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 128 through 141
    Processing helix  chain 'C' and resid 148 through 152
    Processing helix  chain 'C' and resid 198 through 213
      removed outlier: 3.922A  pdb=" N   VAL C 202 " --> pdb=" O   SER C 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 230 through 250
      removed outlier: 4.484A  pdb=" N   ALA C 235 " --> pdb=" O   TYR C 231 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   ASN C 236 " --> pdb=" O   SER C 232 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ALA C 243 " --> pdb=" O   ASP C 239 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   THR C 244 " --> pdb=" O   ARG C 240 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   ASN C 248 " --> pdb=" O   THR C 244 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LYS C 250 " --> pdb=" O   LYS C 246 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 266 through 279
      removed outlier: 3.748A  pdb=" N   GLY C 279 " --> pdb=" O   SER C 275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 282 through 291
      removed outlier: 3.720A  pdb=" N   LYS C 286 " --> pdb=" O   LEU C 282 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   LEU C 288 " --> pdb=" O   VAL C 284 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   LEU C 289 " --> pdb=" O   CYS C 285 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   PHE C 290 " --> pdb=" O   LYS C 286 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 303 through 311
    Processing helix  chain 'D' and resid 3 through 6
    Processing helix  chain 'D' and resid 23 through 32
      removed outlier: 3.885A  pdb=" N   THR D  32 " --> pdb=" O   LYS D  28 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 54 through 60
      removed outlier: 4.497A  pdb=" N   LYS D  59 " --> pdb=" O   GLN D  56 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 74 through 89
      removed outlier: 4.163A  pdb=" N   THR D  78 " --> pdb=" O   THR D  74 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 97 through 102
    Processing helix  chain 'D' and resid 107 through 119
      removed outlier: 3.774A  pdb=" N   LEU D 111 " --> pdb=" O   SER D 107 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 128
      removed outlier: 4.148A  pdb=" N   HIS D 127 " --> pdb=" O   ASP D 123 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 128 through 141
    Processing helix  chain 'D' and resid 198 through 213
      removed outlier: 3.954A  pdb=" N   VAL D 202 " --> pdb=" O   SER D 198 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 230 through 232
      No H-bonds generated for 'chain 'D' and resid 230 through 232'
    Processing helix  chain 'D' and resid 233 through 250
      removed outlier: 3.588A  pdb=" N   HIS D 237 " --> pdb=" O   SER D 233 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   THR D 244 " --> pdb=" O   ARG D 240 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ASN D 248 " --> pdb=" O   THR D 244 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   LYS D 250 " --> pdb=" O   LYS D 246 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 266 through 278
    Processing helix  chain 'D' and resid 282 through 291
      removed outlier: 3.750A  pdb=" N   LYS D 286 " --> pdb=" O   LEU D 282 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   LEU D 288 " --> pdb=" O   VAL D 284 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   LEU D 289 " --> pdb=" O   CYS D 285 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   PHE D 290 " --> pdb=" O   LYS D 286 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 303 through 312
      removed outlier: 3.755A  pdb=" N   VAL D 312 " --> pdb=" O   LYS D 308 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 23 through 33
      removed outlier: 3.751A  pdb=" N   THR E  32 " --> pdb=" O   LYS E  28 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 54 through 60
      removed outlier: 4.555A  pdb=" N   LYS E  59 " --> pdb=" O   GLN E  56 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 74 through 89
      removed outlier: 4.273A  pdb=" N   THR E  78 " --> pdb=" O   THR E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 97 through 102
      removed outlier: 3.673A  pdb=" N   LEU E 102 " --> pdb=" O   VAL E  98 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 107 through 119
      removed outlier: 3.704A  pdb=" N   LEU E 111 " --> pdb=" O   SER E 107 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   GLU E 119 " --> pdb=" O   VAL E 115 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 123 through 127
    Processing helix  chain 'E' and resid 128 through 141
    Processing helix  chain 'E' and resid 148 through 152
    Processing helix  chain 'E' and resid 199 through 213
    Processing helix  chain 'E' and resid 230 through 232
      No H-bonds generated for 'chain 'E' and resid 230 through 232'
    Processing helix  chain 'E' and resid 233 through 247
      removed outlier: 4.346A  pdb=" N   THR E 244 " --> pdb=" O   ARG E 240 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 266 through 279
      removed outlier: 3.557A  pdb=" N   GLY E 279 " --> pdb=" O   SER E 275 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 285 through 289
    Processing helix  chain 'E' and resid 303 through 311
    Processing helix  chain 'F' and resid 3 through 7
      removed outlier: 3.639A  pdb=" N   PHE F   7 " --> pdb=" O   LEU F   4 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 23 through 32
      removed outlier: 3.791A  pdb=" N   THR F  32 " --> pdb=" O   LYS F  28 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 54 through 61
      removed outlier: 3.545A  pdb=" N   PHE F  57 " --> pdb=" O   PRO F  54 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   LYS F  59 " --> pdb=" O   GLN F  56 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   TYR F  61 " --> pdb=" O   LYS F  58 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 74 through 91
      removed outlier: 4.064A  pdb=" N   THR F  78 " --> pdb=" O   THR F  74 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   SER F  90 " --> pdb=" O   GLU F  86 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LEU F  91 " --> pdb=" O   ALA F  87 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 97 through 102
    Processing helix  chain 'F' and resid 107 through 120
      removed outlier: 3.863A  pdb=" N   LEU F 111 " --> pdb=" O   SER F 107 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ASN F 120 " --> pdb=" O   ILE F 116 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 128 through 141
      removed outlier: 3.540A  pdb=" N   LEU F 132 " --> pdb=" O   SER F 128 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 148 through 152
    Processing helix  chain 'F' and resid 198 through 213
      removed outlier: 3.937A  pdb=" N   VAL F 202 " --> pdb=" O   SER F 198 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 230 through 232
      No H-bonds generated for 'chain 'F' and resid 230 through 232'
    Processing helix  chain 'F' and resid 233 through 250
      removed outlier: 3.603A  pdb=" N   ASP F 239 " --> pdb=" O   ALA F 235 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA F 243 " --> pdb=" O   ASP F 239 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   THR F 244 " --> pdb=" O   ARG F 240 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ASN F 248 " --> pdb=" O   THR F 244 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   LYS F 250 " --> pdb=" O   LYS F 246 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 266 through 279
      removed outlier: 3.751A  pdb=" N   GLY F 279 " --> pdb=" O   SER F 275 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 282 through 291
      removed outlier: 3.980A  pdb=" N   LYS F 286 " --> pdb=" O   LEU F 282 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   LEU F 288 " --> pdb=" O   VAL F 284 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   LEU F 289 " --> pdb=" O   CYS F 285 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   PHE F 290 " --> pdb=" O   LYS F 286 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLN F 291 " --> pdb=" O   ARG F 287 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 303 through 311
    Processing helix  chain 'G' and resid 5 through 7
      No H-bonds generated for 'chain 'G' and resid 5 through 7'
    Processing helix  chain 'G' and resid 23 through 32
      removed outlier: 3.564A  pdb=" N   THR G  32 " --> pdb=" O   LYS G  28 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 54 through 61
      removed outlier: 3.618A  pdb=" N   PHE G  57 " --> pdb=" O   PRO G  54 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   LYS G  59 " --> pdb=" O   GLN G  56 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   TYR G  61 " --> pdb=" O   LYS G  58 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 74 through 91
      removed outlier: 4.110A  pdb=" N   THR G  78 " --> pdb=" O   THR G  74 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   SER G  90 " --> pdb=" O   GLU G  86 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LEU G  91 " --> pdb=" O   ALA G  87 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 97 through 102
    Processing helix  chain 'G' and resid 107 through 119
      removed outlier: 3.719A  pdb=" N   LEU G 111 " --> pdb=" O   SER G 107 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ARG G 117 " --> pdb=" O   ASN G 113 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 128 through 141
    Processing helix  chain 'G' and resid 148 through 152
    Processing helix  chain 'G' and resid 199 through 213
    Processing helix  chain 'G' and resid 230 through 250
      removed outlier: 4.483A  pdb=" N   ALA G 235 " --> pdb=" O   TYR G 231 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ASN G 236 " --> pdb=" O   SER G 232 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   THR G 244 " --> pdb=" O   ARG G 240 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ASN G 248 " --> pdb=" O   THR G 244 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LYS G 250 " --> pdb=" O   LYS G 246 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 266 through 279
      removed outlier: 3.776A  pdb=" N   GLY G 279 " --> pdb=" O   SER G 275 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 282 through 291
      removed outlier: 3.528A  pdb=" N   LYS G 286 " --> pdb=" O   LEU G 282 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   LEU G 288 " --> pdb=" O   VAL G 284 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   LEU G 289 " --> pdb=" O   CYS G 285 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   PHE G 290 " --> pdb=" O   LYS G 286 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 303 through 311
    Processing helix  chain 'U' and resid 3 through 6
    Processing helix  chain 'U' and resid 23 through 32
      removed outlier: 3.683A  pdb=" N   THR U  32 " --> pdb=" O   LYS U  28 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 54 through 61
      removed outlier: 4.492A  pdb=" N   LYS U  59 " --> pdb=" O   GLN U  56 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   TYR U  61 " --> pdb=" O   LYS U  58 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 75 through 89
    Processing helix  chain 'U' and resid 97 through 102
      removed outlier: 3.726A  pdb=" N   LEU U 102 " --> pdb=" O   VAL U  98 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 107 through 120
      removed outlier: 3.699A  pdb=" N   LEU U 111 " --> pdb=" O   SER U 107 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ASN U 120 " --> pdb=" O   ILE U 116 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 128 through 141
    Processing helix  chain 'U' and resid 199 through 213
    Processing helix  chain 'U' and resid 230 through 250
      removed outlier: 4.508A  pdb=" N   ALA U 235 " --> pdb=" O   TYR U 231 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   ASN U 236 " --> pdb=" O   SER U 232 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   THR U 244 " --> pdb=" O   ARG U 240 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   PHE U 245 " --> pdb=" O   VAL U 241 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ASN U 248 " --> pdb=" O   THR U 244 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LYS U 250 " --> pdb=" O   LYS U 246 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 266 through 278
    Processing helix  chain 'U' and resid 282 through 291
      removed outlier: 3.687A  pdb=" N   LYS U 286 " --> pdb=" O   LEU U 282 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   LEU U 288 " --> pdb=" O   VAL U 284 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   LEU U 289 " --> pdb=" O   CYS U 285 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   PHE U 290 " --> pdb=" O   LYS U 286 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 303 through 312
      removed outlier: 3.519A  pdb=" N   VAL U 312 " --> pdb=" O   LYS U 308 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 12
    Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 46
      removed outlier: 3.519A  pdb=" N   SER A  46 " --> pdb=" O   GLY A  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 160
      removed outlier: 6.717A  pdb=" N   ILE A 157 " --> pdb=" O   LYS A 168 " (cutoff:3.500A)
      removed outlier: 5.953A  pdb=" N   LYS A 168 " --> pdb=" O   ILE A 157 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   PHE A 159 " --> pdb=" O   MET A 166 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   GLU A 186 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 9 through 12
    Processing sheet with id=AA5, first strand: chain 'B' and resid 44 through 46
      removed outlier: 3.514A  pdb=" N   SER B  46 " --> pdb=" O   GLY B  50 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 160
      removed outlier: 6.507A  pdb=" N   ILE B 157 " --> pdb=" O   LYS B 168 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   LYS B 168 " --> pdb=" O   ILE B 157 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   PHE B 159 " --> pdb=" O   MET B 166 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   GLU B 186 " --> pdb=" O   LEU B 169 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 8 through 12
    Processing sheet with id=AA8, first strand: chain 'C' and resid 44 through 46
    Processing sheet with id=AA9, first strand: chain 'C' and resid 156 through 160
      removed outlier: 6.595A  pdb=" N   ILE C 157 " --> pdb=" O   LYS C 168 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   LYS C 168 " --> pdb=" O   ILE C 157 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   PHE C 159 " --> pdb=" O   MET C 166 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   GLU C 186 " --> pdb=" O   LEU C 169 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 217 through 220
      removed outlier: 3.510A  pdb=" N   VAL C 229 " --> pdb=" O   ALA C 217 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 8 through 12
    Processing sheet with id=AB3, first strand: chain 'D' and resid 44 through 46
    Processing sheet with id=AB4, first strand: chain 'D' and resid 156 through 160
      removed outlier: 6.387A  pdb=" N   ILE D 157 " --> pdb=" O   LYS D 168 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   LYS D 168 " --> pdb=" O   ILE D 157 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   PHE D 159 " --> pdb=" O   MET D 166 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   GLU D 186 " --> pdb=" O   LEU D 169 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 2 through 3
    Processing sheet with id=AB6, first strand: chain 'E' and resid 8 through 12
    Processing sheet with id=AB7, first strand: chain 'E' and resid 44 through 46
    Processing sheet with id=AB8, first strand: chain 'E' and resid 156 through 160
      removed outlier: 6.421A  pdb=" N   ILE E 157 " --> pdb=" O   LYS E 168 " (cutoff:3.500A)
      removed outlier: 5.937A  pdb=" N   LYS E 168 " --> pdb=" O   ILE E 157 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   PHE E 159 " --> pdb=" O   MET E 166 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   GLU E 186 " --> pdb=" O   LEU E 169 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 9 through 12
    Processing sheet with id=AC1, first strand: chain 'F' and resid 44 through 46
    Processing sheet with id=AC2, first strand: chain 'F' and resid 156 through 160
      removed outlier: 6.475A  pdb=" N   ILE F 157 " --> pdb=" O   LYS F 168 " (cutoff:3.500A)
      removed outlier: 5.944A  pdb=" N   LYS F 168 " --> pdb=" O   ILE F 157 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   PHE F 159 " --> pdb=" O   MET F 166 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   GLU F 186 " --> pdb=" O   LEU F 169 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'G' and resid 2 through 3
    Processing sheet with id=AC4, first strand: chain 'G' and resid 9 through 12
    Processing sheet with id=AC5, first strand: chain 'G' and resid 44 through 46
    Processing sheet with id=AC6, first strand: chain 'G' and resid 156 through 160
      removed outlier: 6.484A  pdb=" N   ILE G 157 " --> pdb=" O   LYS G 168 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   LYS G 168 " --> pdb=" O   ILE G 157 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   PHE G 159 " --> pdb=" O   MET G 166 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   GLU G 186 " --> pdb=" O   LEU G 169 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'U' and resid 8 through 12
    Processing sheet with id=AC8, first strand: chain 'U' and resid 44 through 46
      removed outlier: 3.712A  pdb=" N   SER U  46 " --> pdb=" O   GLY U  50 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'U' and resid 156 through 160
      removed outlier: 6.280A  pdb=" N   ILE U 157 " --> pdb=" O   LYS U 168 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   LYS U 168 " --> pdb=" O   ILE U 157 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   PHE U 159 " --> pdb=" O   MET U 166 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   GLU U 186 " --> pdb=" O   LEU U 169 " (cutoff:3.500A)

    790 hydrogen bonds defined for protein.
    2160 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: 5.67

  Time building geometry restraints manager: 9.04 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 6516
        1.34 -     1.46: 4261
        1.46 -     1.58: 9815
        1.58 -     1.69: 0
        1.69 -     1.81: 208
  Bond restraints: 20800
  Sorted by residual:
  bond pdb=" CA  SER D 232 "
       pdb=" C   SER D 232 "
    ideal  model  delta    sigma   weight residual
    1.523  1.491  0.032 1.34e-02 5.57e+03 5.83e+00
  bond pdb=" CA  SER A 232 "
       pdb=" C   SER A 232 "
    ideal  model  delta    sigma   weight residual
    1.523  1.491  0.032 1.34e-02 5.57e+03 5.71e+00
  bond pdb=" CA  ARG U 210 "
       pdb=" C   ARG U 210 "
    ideal  model  delta    sigma   weight residual
    1.522  1.482  0.040 1.72e-02 3.38e+03 5.44e+00
  bond pdb=" CA  ARG E 210 "
       pdb=" C   ARG E 210 "
    ideal  model  delta    sigma   weight residual
    1.523  1.497  0.026 1.41e-02 5.03e+03 3.31e+00
  bond pdb=" C   ILE D 264 "
       pdb=" N   ILE D 265 "
    ideal  model  delta    sigma   weight residual
    1.334  1.312  0.022 1.29e-02 6.01e+03 2.89e+00
  ... (remaining 20795 not shown)

  Histogram of bond angle deviations from ideal:
       99.32 -   106.25: 446
      106.25 -   113.18: 11493
      113.18 -   120.11: 7161
      120.11 -   127.04: 8783
      127.04 -   133.97: 205
  Bond angle restraints: 28088
  Sorted by residual:
  angle pdb=" C   GLN A 160 "
        pdb=" N   ASN A 161 "
        pdb=" CA  ASN A 161 "
      ideal   model   delta    sigma   weight residual
     121.90  116.31    5.59 1.26e+00 6.30e-01 1.97e+01
  angle pdb=" C   GLN D 160 "
        pdb=" N   ASN D 161 "
        pdb=" CA  ASN D 161 "
      ideal   model   delta    sigma   weight residual
     121.90  116.60    5.30 1.26e+00 6.30e-01 1.77e+01
  angle pdb=" C   GLN C 160 "
        pdb=" N   ASN C 161 "
        pdb=" CA  ASN C 161 "
      ideal   model   delta    sigma   weight residual
     121.90  116.79    5.11 1.26e+00 6.30e-01 1.65e+01
  angle pdb=" N   ASP G  41 "
        pdb=" CA  ASP G  41 "
        pdb=" C   ASP G  41 "
      ideal   model   delta    sigma   weight residual
     114.09  108.05    6.04 1.55e+00 4.16e-01 1.52e+01
  angle pdb=" N   ASP C  15 "
        pdb=" CA  ASP C  15 "
        pdb=" C   ASP C  15 "
      ideal   model   delta    sigma   weight residual
     114.75  109.85    4.90 1.26e+00 6.30e-01 1.51e+01
  ... (remaining 28083 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.70: 11396
       17.70 -    35.39: 1012
       35.39 -    53.09: 158
       53.09 -    70.78: 55
       70.78 -    88.48: 27
  Dihedral angle restraints: 12648
    sinusoidal: 5208
      harmonic: 7440
  Sorted by residual:
  dihedral pdb=" CA  MET G  40 "
           pdb=" C   MET G  40 "
           pdb=" N   ASP G  41 "
           pdb=" CA  ASP G  41 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.28   19.72     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  TYR G  17 "
           pdb=" C   TYR G  17 "
           pdb=" N   LYS G  18 "
           pdb=" CA  LYS G  18 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.93   17.07     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  SER C  46 "
           pdb=" C   SER C  46 "
           pdb=" N   ILE C  47 "
           pdb=" CA  ILE C  47 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.80  -16.20     0      5.00e+00 4.00e-02 1.05e+01
  ... (remaining 12645 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 2051
       0.037 -    0.073: 859
       0.073 -    0.110: 206
       0.110 -    0.147: 19
       0.147 -    0.183: 1
  Chirality restraints: 3136
  Sorted by residual:
  chirality pdb=" CB  THR U 170 "
            pdb=" CA  THR U 170 "
            pdb=" OG1 THR U 170 "
            pdb=" CG2 THR U 170 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.18 2.00e-01 2.50e+01 8.41e-01
  chirality pdb=" CA  ILE G 228 "
            pdb=" N   ILE G 228 "
            pdb=" C   ILE G 228 "
            pdb=" CB  ILE G 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.75e-01
  chirality pdb=" CA  ILE U 228 "
            pdb=" N   ILE U 228 "
            pdb=" C   ILE U 228 "
            pdb=" CB  ILE U 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.55e-01
  ... (remaining 3133 not shown)

  Planarity restraints: 3560
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 294 "    0.022 5.00e-02 4.00e+02   3.39e-02 1.84e+00
        pdb=" N   PRO C 295 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO C 295 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO C 295 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR E 231 "   -0.007 2.00e-02 2.50e+03   1.35e-02 1.83e+00
        pdb=" C   TYR E 231 "    0.023 2.00e-02 2.50e+03
        pdb=" O   TYR E 231 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   SER E 232 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR F 231 "   -0.007 2.00e-02 2.50e+03   1.35e-02 1.81e+00
        pdb=" C   TYR F 231 "    0.023 2.00e-02 2.50e+03
        pdb=" O   TYR F 231 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   SER F 232 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 3557 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 2359
        2.74 -     3.28: 21218
        3.28 -     3.82: 31813
        3.82 -     4.36: 37885
        4.36 -     4.90: 62861
  Nonbonded interactions: 156136
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU E  13 "
            pdb=" OG  SER E  16 "
     model   vdw
     2.205 2.440
  nonbonded pdb=" OH  TYR E 231 "
            pdb=" NZ  LYS U 308 "
     model   vdw
     2.259 2.520
  nonbonded pdb=" ND2 ASN C  62 "
            pdb=" OD1 ASN C  71 "
     model   vdw
     2.265 2.520
  nonbonded pdb=" ND2 ASN G  62 "
            pdb=" OD1 ASN G  71 "
     model   vdw
     2.265 2.520
  nonbonded pdb=" OD1 ASN A 161 "
            pdb=" ND1 HIS A 201 "
     model   vdw
     2.269 2.520
  ... (remaining 156131 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 'U'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     120      5.16       5
     C   13064      2.51       5
     N    3456      2.21       5
     O    3728      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.360
  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:             0.020
  Extract box with map and model:          3.970
  Check model and map are aligned:         0.300
  Convert atoms to be neutral:             0.160
  Process input model:                     51.190
  Find NCS groups from input model:        1.310
  Set up NCS constraints:                  0.100
  Set refine NCS operators:                0.000
  Set scattering table:                    0.010
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   60.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
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      :  0.004   0.040  20800  Z= 0.258
  Angle     :  0.659   6.897  28088  Z= 0.400
  Chirality :  0.040   0.183   3136
  Planarity :  0.003   0.034   3560
  Dihedral  : 14.592  88.477   7800
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.16 (0.13), residues: 2488
  helix: -2.31 (0.13), residues: 800
  sheet: -2.74 (0.25), residues: 280
  loop : -3.15 (0.14), residues: 1408

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

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

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  549 residues out of total 2272 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 549
  time to evaluate  : 2.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 549
  average time/residue: 0.3583
  time to fit residues: 288.3609
Evaluate side-chains
  414 residues out of total 2272 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 414
  time to evaluate  : 2.427 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 3.3309
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 209 optimal weight:    5.9990
   chunk 187 optimal weight:    6.9990
   chunk 104 optimal weight:    4.9990
   chunk 64 optimal weight:    0.6980
   chunk 126 optimal weight:    3.9990
   chunk 100 optimal weight:    1.9990
   chunk 194 optimal weight:    0.4980
   chunk 75 optimal weight:    1.9990
   chunk 118 optimal weight:    6.9990
   chunk 144 optimal weight:    0.9990
   chunk 225 optimal weight:    0.0570
   overall best weight:    0.8502

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN
A  64 ASN
A  71 ASN
** A  89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 110 HIS
A 174 HIS
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  71 ASN
B 110 HIS
B 122 GLN
B 142 GLN
B 192 ASN
** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 298 ASN
C  14 ASN
C  23 ASN
C  56 GLN
C  64 ASN
C 122 GLN
C 142 GLN
C 175 GLN
** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 258 ASN
C 268 ASN
D  64 ASN
D  89 ASN
D 110 HIS
D 142 GLN
D 214 ASN
D 237 HIS
E  23 ASN
** E  62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 110 HIS
E 174 HIS
E 183 ASN
E 278 GLN
E 280 ASN
F  23 ASN
F  62 ASN
F  89 ASN
F 100 ASN
F 142 GLN
F 221 HIS
G  14 ASN
G  23 ASN
G 142 GLN
G 298 ASN
U  23 ASN
U  64 ASN
U  71 ASN
U  95 GLN
U 142 GLN
U 175 GLN
U 183 ASN
U 237 HIS

Total number of N/Q/H flips: 50

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.1867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.052  20800  Z= 0.170
  Angle     :  0.550   8.372  28088  Z= 0.289
  Chirality :  0.039   0.163   3136
  Planarity :  0.004   0.080   3560
  Dihedral  :  5.118  65.926   2688
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer Outliers :  2.73 %
  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: -2.47 (0.15), residues: 2488
  helix: -0.34 (0.17), residues: 832
  sheet: -2.57 (0.25), residues: 296
  loop : -2.33 (0.15), residues: 1360

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

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

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  512 residues out of total 2272 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 62
    poor density    : 450
  time to evaluate  : 2.424 
Fit side-chains
   revert: symmetry clash
  outliers start: 62
  outliers final: 43
  residues processed: 477
  average time/residue: 0.3289
  time to fit residues: 237.0947
Evaluate side-chains
  438 residues out of total 2272 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 395
  time to evaluate  : 2.443 
Switching outliers to nearest non-outliers
  outliers start: 43
  outliers final: 0
  residues processed: 43
  average time/residue: 0.1760
  time to fit residues: 17.7953
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 125 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 187 optimal weight:    4.9990
   chunk 153 optimal weight:    5.9990
   chunk 62 optimal weight:   10.0000
   chunk 225 optimal weight:    4.9990
   chunk 243 optimal weight:    0.4980
   chunk 200 optimal weight:    9.9990
   chunk 223 optimal weight:    0.0000
   chunk 76 optimal weight:    9.9990
   chunk 180 optimal weight:   10.0000
   overall best weight:    2.6990

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

Flipped N/Q/H residues before XYZ refinement:
A 212 GLN
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 HIS
B 298 ASN
D 214 ASN
** E  62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 183 ASN
E 212 GLN
** E 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 278 GLN
F 160 GLN
U 110 HIS
U 160 GLN
** U 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
U 291 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.049  20800  Z= 0.290
  Angle     :  0.588   7.376  28088  Z= 0.304
  Chirality :  0.041   0.211   3136
  Planarity :  0.004   0.082   3560
  Dihedral  :  5.001  62.652   2688
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer Outliers :  2.82 %
  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: -2.13 (0.16), residues: 2488
  helix: -0.04 (0.17), residues: 832
  sheet: -2.37 (0.26), residues: 296
  loop : -2.14 (0.16), residues: 1360

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

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

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  473 residues out of total 2272 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 64
    poor density    : 409
  time to evaluate  : 2.598 
Fit side-chains
   revert: symmetry clash
  outliers start: 64
  outliers final: 42
  residues processed: 445
  average time/residue: 0.2989
  time to fit residues: 206.1159
Evaluate side-chains
  422 residues out of total 2272 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 380
  time to evaluate  : 2.334 
Switching outliers to nearest non-outliers
  outliers start: 42
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1746
  time to fit residues: 17.1055
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 222 optimal weight:    0.5980
   chunk 169 optimal weight:    1.9990
   chunk 117 optimal weight:    5.9990
   chunk 24 optimal weight:    9.9990
   chunk 107 optimal weight:    6.9990
   chunk 151 optimal weight:    8.9990
   chunk 226 optimal weight:    4.9990
   chunk 239 optimal weight:    5.9990
   chunk 118 optimal weight:    5.9990
   chunk 214 optimal weight:    8.9990
   chunk 64 optimal weight:    0.8980
   overall best weight:    2.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 192 ASN
** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 183 ASN
** E 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.064  20800  Z= 0.307
  Angle     :  0.597   7.599  28088  Z= 0.308
  Chirality :  0.041   0.179   3136
  Planarity :  0.004   0.090   3560
  Dihedral  :  4.977  59.319   2688
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.84 %
    Favored  : 92.16 %
  Rotamer Outliers :  3.35 %
  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: -1.89 (0.16), residues: 2488
  helix:  0.13 (0.17), residues: 832
  sheet: -1.97 (0.27), residues: 280
  loop : -2.05 (0.16), residues: 1376

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

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

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  482 residues out of total 2272 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 76
    poor density    : 406
  time to evaluate  : 2.450 
Fit side-chains
   revert: symmetry clash
  outliers start: 76
  outliers final: 51
  residues processed: 440
  average time/residue: 0.2978
  time to fit residues: 205.5562
Evaluate side-chains
  422 residues out of total 2272 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 371
  time to evaluate  : 2.495 
Switching outliers to nearest non-outliers
  outliers start: 51
  outliers final: 0
  residues processed: 51
  average time/residue: 0.1798
  time to fit residues: 20.6211
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 199 optimal weight:    2.9990
   chunk 136 optimal weight:    0.0570
   chunk 3 optimal weight:    8.9990
   chunk 178 optimal weight:    0.9990
   chunk 98 optimal weight:    5.9990
   chunk 204 optimal weight:    0.5980
   chunk 165 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 122 optimal weight:    7.9990
   chunk 215 optimal weight:   20.0000
   chunk 60 optimal weight:   20.0000
   overall best weight:    1.9304

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  62 ASN
B  71 ASN
C 110 HIS
** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 214 ASN
** E  62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 183 ASN
** E 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.082  20800  Z= 0.237
  Angle     :  0.572   8.264  28088  Z= 0.293
  Chirality :  0.041   0.223   3136
  Planarity :  0.004   0.097   3560
  Dihedral  :  4.821  55.443   2688
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Rotamer Outliers :  2.20 %
  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: -1.57 (0.16), residues: 2488
  helix:  0.49 (0.18), residues: 824
  sheet: -1.87 (0.27), residues: 280
  loop : -1.88 (0.16), residues: 1384

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

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

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  459 residues out of total 2272 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 50
    poor density    : 409
  time to evaluate  : 2.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 50
  outliers final: 29
  residues processed: 436
  average time/residue: 0.3056
  time to fit residues: 206.2821
Evaluate side-chains
  400 residues out of total 2272 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 371
  time to evaluate  : 2.435 
Switching outliers to nearest non-outliers
  outliers start: 29
  outliers final: 0
  residues processed: 29
  average time/residue: 0.1700
  time to fit residues: 12.7316
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 80 optimal weight:    0.0980
   chunk 215 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9980
   chunk 140 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 239 optimal weight:    1.9990
   chunk 199 optimal weight:    3.9990
   chunk 111 optimal weight:    6.9990
   chunk 19 optimal weight:   10.0000
   chunk 79 optimal weight:    0.7980
   chunk 125 optimal weight:    0.6980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 142 GLN
** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 183 ASN
** G  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 212 GLN
U 160 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.038  20800  Z= 0.165
  Angle     :  0.555   8.831  28088  Z= 0.281
  Chirality :  0.040   0.201   3136
  Planarity :  0.003   0.065   3560
  Dihedral  :  4.570  50.763   2688
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer Outliers :  1.80 %
  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: -1.22 (0.16), residues: 2488
  helix:  0.85 (0.18), residues: 824
  sheet: -1.82 (0.27), residues: 280
  loop : -1.68 (0.16), residues: 1384

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

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

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  447 residues out of total 2272 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 406
  time to evaluate  : 2.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 41
  outliers final: 25
  residues processed: 426
  average time/residue: 0.3154
  time to fit residues: 205.6959
Evaluate side-chains
  410 residues out of total 2272 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 385
  time to evaluate  : 2.686 
Switching outliers to nearest non-outliers
  outliers start: 25
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1850
  time to fit residues: 12.4648
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 231 optimal weight:    9.9990
   chunk 27 optimal weight:    0.9980
   chunk 136 optimal weight:    0.9980
   chunk 175 optimal weight:    0.8980
   chunk 135 optimal weight:    4.9990
   chunk 201 optimal weight:    0.9980
   chunk 133 optimal weight:    3.9990
   chunk 239 optimal weight:    7.9990
   chunk 149 optimal weight:   10.0000
   chunk 145 optimal weight:    1.9990
   chunk 110 optimal weight:    6.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 214 ASN
** E  62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 183 ASN
** G  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  66 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.038  20800  Z= 0.178
  Angle     :  0.559   9.195  28088  Z= 0.283
  Chirality :  0.040   0.184   3136
  Planarity :  0.003   0.052   3560
  Dihedral  :  4.390  45.567   2688
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer Outliers :  1.28 %
  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: -1.06 (0.17), residues: 2488
  helix:  1.00 (0.18), residues: 824
  sheet: -1.97 (0.27), residues: 296
  loop : -1.51 (0.16), residues: 1368

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

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

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  434 residues out of total 2272 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 405
  time to evaluate  : 2.658 
Fit side-chains
   revert: symmetry clash
  outliers start: 29
  outliers final: 21
  residues processed: 419
  average time/residue: 0.3223
  time to fit residues: 206.4655
Evaluate side-chains
  402 residues out of total 2272 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 381
  time to evaluate  : 2.579 
Switching outliers to nearest non-outliers
  outliers start: 21
  outliers final: 0
  residues processed: 21
  average time/residue: 0.1807
  time to fit residues: 10.6992
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 147 optimal weight:    0.8980
   chunk 95 optimal weight:    0.2980
   chunk 142 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 151 optimal weight:    8.9990
   chunk 162 optimal weight:    5.9990
   chunk 118 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 187 optimal weight:    8.9990
   chunk 217 optimal weight:   10.0000
   overall best weight:    2.4386

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 183 ASN
F  23 ASN
** F 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 183 ASN
U  66 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.3024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.118  20800  Z= 0.277
  Angle     :  0.609   9.231  28088  Z= 0.310
  Chirality :  0.041   0.178   3136
  Planarity :  0.004   0.118   3560
  Dihedral  :  4.484  42.583   2688
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer Outliers :  1.85 %
  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: -1.01 (0.17), residues: 2488
  helix:  0.91 (0.18), residues: 832
  sheet: -1.71 (0.28), residues: 280
  loop : -1.48 (0.16), residues: 1376

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

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

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  420 residues out of total 2272 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 378
  time to evaluate  : 2.457 
Fit side-chains
  outliers start: 42
  outliers final: 32
  residues processed: 394
  average time/residue: 0.3241
  time to fit residues: 195.8514
Evaluate side-chains
  401 residues out of total 2272 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 369
  time to evaluate  : 2.371 
Switching outliers to nearest non-outliers
  outliers start: 32
  outliers final: 0
  residues processed: 32
  average time/residue: 0.1851
  time to fit residues: 14.5518
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 228 optimal weight:    0.6980
   chunk 208 optimal weight:    5.9990
   chunk 222 optimal weight:    0.9980
   chunk 134 optimal weight:    1.9990
   chunk 97 optimal weight:    0.0980
   chunk 174 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 201 optimal weight:    0.7980
   chunk 210 optimal weight:   10.0000
   chunk 221 optimal weight:    0.9990
   chunk 146 optimal weight:    4.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 174 HIS
** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 174 HIS
G  66 ASN
U  66 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.3271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.086  20800  Z= 0.161
  Angle     :  0.574   9.903  28088  Z= 0.287
  Chirality :  0.040   0.167   3136
  Planarity :  0.003   0.094   3560
  Dihedral  :  4.298  37.184   2688
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer Outliers :  0.75 %
  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: -0.85 (0.17), residues: 2488
  helix:  1.19 (0.19), residues: 824
  sheet: -1.99 (0.27), residues: 296
  loop : -1.36 (0.16), residues: 1368

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

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

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  411 residues out of total 2272 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 394
  time to evaluate  : 2.706 
Fit side-chains
  outliers start: 17
  outliers final: 7
  residues processed: 403
  average time/residue: 0.3297
  time to fit residues: 203.2411
Evaluate side-chains
  387 residues out of total 2272 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 380
  time to evaluate  : 2.645 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.1749
  time to fit residues: 5.8968
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 235 optimal weight:    0.3980
   chunk 143 optimal weight:    0.6980
   chunk 111 optimal weight:    0.4980
   chunk 163 optimal weight:    1.9990
   chunk 247 optimal weight:    9.9990
   chunk 227 optimal weight:    6.9990
   chunk 196 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 151 optimal weight:    9.9990
   chunk 120 optimal weight:    9.9990
   chunk 156 optimal weight:    0.7980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 214 ASN
** E  62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 182 GLN
E 183 ASN
** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 298 ASN
G 183 ASN
U  66 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.3414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.169  20800  Z= 0.191
  Angle     :  0.605  16.002  28088  Z= 0.307
  Chirality :  0.041   0.293   3136
  Planarity :  0.004   0.149   3560
  Dihedral  :  4.206  32.560   2688
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer Outliers :  0.57 %
  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: -0.78 (0.17), residues: 2488
  helix:  1.21 (0.19), residues: 824
  sheet: -1.90 (0.27), residues: 296
  loop : -1.30 (0.16), residues: 1368

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

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

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  408 residues out of total 2272 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 395
  time to evaluate  : 2.525 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 9
  residues processed: 398
  average time/residue: 0.3358
  time to fit residues: 201.9996
Evaluate side-chains
  384 residues out of total 2272 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 375
  time to evaluate  : 2.480 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.1704
  time to fit residues: 6.3712
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 209 optimal weight:    6.9990
   chunk 60 optimal weight:    9.9990
   chunk 181 optimal weight:    0.2980
   chunk 29 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 197 optimal weight:    0.9980
   chunk 82 optimal weight:    7.9990
   chunk 202 optimal weight:    0.6980
   chunk 24 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0770
   chunk 173 optimal weight:    7.9990
   overall best weight:    1.2140

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  62 ASN
** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 100 ASN
D 214 ASN
** E  62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 183 ASN
** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
U  66 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.148180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.117085 restraints weight = 34850.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.120690 restraints weight = 21783.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.123072 restraints weight = 16420.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.3452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.131  20800  Z= 0.199
  Angle     :  0.591  11.520  28088  Z= 0.298
  Chirality :  0.041   0.174   3136
  Planarity :  0.004   0.123   3560
  Dihedral  :  4.147  29.873   2688
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer Outliers :  0.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.75 (0.17), residues: 2488
  helix:  1.20 (0.18), residues: 824
  sheet: -1.90 (0.27), residues: 296
  loop : -1.26 (0.17), residues: 1368

===============================================================================
Job complete
usr+sys time: 4231.06 seconds
wall clock time: 78 minutes 20.86 seconds (4700.86 seconds total)