Starting phenix.real_space_refine
on Sun Mar 24 18:13:33 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkh_24497/03_2024/7rkh_24497_trim_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkh_24497/03_2024/7rkh_24497.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkh_24497/03_2024/7rkh_24497_trim_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkh_24497/03_2024/7rkh_24497_trim_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkh_24497/03_2024/7rkh_24497_trim_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkh_24497/03_2024/7rkh_24497.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkh_24497/03_2024/7rkh_24497.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkh_24497/03_2024/7rkh_24497_trim_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkh_24497/03_2024/7rkh_24497_trim_updated.pdb"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.189
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 8096 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     P      24      5.49       5
     Mg      8      5.21       5
     S      80      5.16       5
     C   11176      2.51       5
     N    3056      2.21       5
     O    3444      1.98       5
     H   17564      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "D GLU   57": "OE1" <-> "OE2"
    Residue "D GLU   66": "OE1" <-> "OE2"
    Residue "D ASP   68": "OD1" <-> "OD2"
    Residue "D TYR   77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D ARG  100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "D ASP  134": "OD1" <-> "OD2"
    Residue "D GLU  161": "OE1" <-> "OE2"
    Residue "D GLU  169": "OE1" <-> "OE2"
    Residue "D PHE  231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D GLU  237": "OE1" <-> "OE2"
    Residue "D TYR  249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D ASP  262": "OD1" <-> "OD2"
    Residue "D ARG  267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "D GLU  291": "OE1" <-> "OE2"
    Residue "D ASP  301": "OD1" <-> "OD2"
    Residue "D GLU  327": "OE1" <-> "OE2"
    Residue "D ARG  334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "D GLU  348": "OE1" <-> "OE2"
    Residue "D PHE  359": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D PHE  378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D ARG  381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "D ARG  394": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "D PHE  400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D PHE  414": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D GLU  432": "OE1" <-> "OE2"
    Residue "D GLU  438": "OE1" <-> "OE2"
    Residue "D TYR  493": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D GLU  494": "OE1" <-> "OE2"
    Residue "D GLU  504": "OE1" <-> "OE2"
    Residue "D PHE  523": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D GLU  524": "OE1" <-> "OE2"
    Residue "D GLU  539": "OE1" <-> "OE2"
    Residue "D GLU  546": "OE1" <-> "OE2"
    Residue "D ASP  568": "OD1" <-> "OD2"
    Residue "A GLU   57": "OE1" <-> "OE2"
    Residue "A GLU   66": "OE1" <-> "OE2"
    Residue "A ASP   68": "OD1" <-> "OD2"
    Residue "A TYR   77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG  100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP  134": "OD1" <-> "OD2"
    Residue "A GLU  161": "OE1" <-> "OE2"
    Residue "A GLU  169": "OE1" <-> "OE2"
    Residue "A PHE  231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  237": "OE1" <-> "OE2"
    Residue "A TYR  249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  262": "OD1" <-> "OD2"
    Residue "A ARG  267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A GLU  291": "OE1" <-> "OE2"
    Residue "A ASP  301": "OD1" <-> "OD2"
    Residue "A GLU  327": "OE1" <-> "OE2"
    Residue "A ARG  334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A GLU  348": "OE1" <-> "OE2"
    Residue "A PHE  359": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE  378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG  381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  394": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A PHE  400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE  414": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  432": "OE1" <-> "OE2"
    Residue "A GLU  438": "OE1" <-> "OE2"
    Residue "A TYR  493": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  494": "OE1" <-> "OE2"
    Residue "A GLU  504": "OE1" <-> "OE2"
    Residue "A PHE  523": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  524": "OE1" <-> "OE2"
    Residue "A GLU  539": "OE1" <-> "OE2"
    Residue "A GLU  546": "OE1" <-> "OE2"
    Residue "A ASP  568": "OD1" <-> "OD2"
    Residue "B GLU   57": "OE1" <-> "OE2"
    Residue "B GLU   66": "OE1" <-> "OE2"
    Residue "B ASP   68": "OD1" <-> "OD2"
    Residue "B TYR   77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B ARG  100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B ASP  134": "OD1" <-> "OD2"
    Residue "B GLU  161": "OE1" <-> "OE2"
    Residue "B GLU  169": "OE1" <-> "OE2"
    Residue "B PHE  231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B GLU  237": "OE1" <-> "OE2"
    Residue "B TYR  249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B ASP  262": "OD1" <-> "OD2"
    Residue "B ARG  267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B GLU  291": "OE1" <-> "OE2"
    Residue "B ASP  301": "OD1" <-> "OD2"
    Residue "B GLU  327": "OE1" <-> "OE2"
    Residue "B ARG  334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B GLU  348": "OE1" <-> "OE2"
    Residue "B PHE  359": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B PHE  378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B ARG  381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B ARG  394": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B PHE  400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B PHE  414": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B GLU  432": "OE1" <-> "OE2"
    Residue "B GLU  438": "OE1" <-> "OE2"
    Residue "B TYR  493": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B GLU  494": "OE1" <-> "OE2"
    Residue "B GLU  504": "OE1" <-> "OE2"
    Residue "B PHE  523": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B GLU  524": "OE1" <-> "OE2"
    Residue "B GLU  539": "OE1" <-> "OE2"
    Residue "B GLU  546": "OE1" <-> "OE2"
    Residue "B ASP  568": "OD1" <-> "OD2"
    Residue "C GLU   57": "OE1" <-> "OE2"
    Residue "C GLU   66": "OE1" <-> "OE2"
    Residue "C ASP   68": "OD1" <-> "OD2"
    Residue "C TYR   77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C ARG  100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "C ASP  134": "OD1" <-> "OD2"
    Residue "C GLU  161": "OE1" <-> "OE2"
    Residue "C GLU  169": "OE1" <-> "OE2"
    Residue "C PHE  231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C GLU  237": "OE1" <-> "OE2"
    Residue "C TYR  249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C ASP  262": "OD1" <-> "OD2"
    Residue "C ARG  267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "C GLU  291": "OE1" <-> "OE2"
    Residue "C ASP  301": "OD1" <-> "OD2"
    Residue "C GLU  327": "OE1" <-> "OE2"
    Residue "C ARG  334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "C GLU  348": "OE1" <-> "OE2"
    Residue "C PHE  359": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C PHE  378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C ARG  381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "C ARG  394": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "C PHE  400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C PHE  414": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C GLU  432": "OE1" <-> "OE2"
    Residue "C GLU  438": "OE1" <-> "OE2"
    Residue "C TYR  493": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C GLU  494": "OE1" <-> "OE2"
    Residue "C GLU  504": "OE1" <-> "OE2"
    Residue "C PHE  523": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C GLU  524": "OE1" <-> "OE2"
    Residue "C GLU  539": "OE1" <-> "OE2"
    Residue "C GLU  546": "OE1" <-> "OE2"
    Residue "C ASP  568": "OD1" <-> "OD2"
  Time to flip residues: 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 35352
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "D"
      Number of atoms: 8776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 559, 8776
          Classifications: {'peptide': 559}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 534}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 8776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 559, 8776
          Classifications: {'peptide': 559}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 534}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 8776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 559, 8776
          Classifications: {'peptide': 559}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 534}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 8776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 559, 8776
          Classifications: {'peptide': 559}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 534}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 62
          Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "A"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 62
          Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 62
          Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "C"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 62
          Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 15.68, per 1000 atoms: 0.44
  Number of scatterers: 35352
  At special positions: 0
  Unit cell: (120.75, 103.95, 131.25, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      80     16.00
     P      24     15.00
     Mg      8     11.99
     O    3444      8.00
     N    3056      7.00
     C   11176      6.00
     H   17564      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 29.69
  Conformation dependent library (CDL) restraints added in 3.6 seconds
  

  4440 Ramachandran restraints generated.
    2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4096

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      104 helices and 20 sheets defined
      44.5% alpha, 14.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 6.97
  Creating SS restraints...
    Processing helix  chain 'D' and resid 16 through 30
      removed outlier: 3.646A  pdb=" N   LEU D  30 " --> pdb=" O   LEU D  26 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 69 through 78
    Processing helix  chain 'D' and resid 84 through 86
      No H-bonds generated for 'chain 'D' and resid 84 through 86'
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 116 through 130
      removed outlier: 3.692A  pdb=" N   LYS D 130 " --> pdb=" O   GLN D 126 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 169
      removed outlier: 3.992A  pdb=" N   PHE D 168 " --> pdb=" O   ARG D 164 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 172 through 174
      No H-bonds generated for 'chain 'D' and resid 172 through 174'
    Processing helix  chain 'D' and resid 193 through 205
    Processing helix  chain 'D' and resid 222 through 231
    Processing helix  chain 'D' and resid 236 through 238
      No H-bonds generated for 'chain 'D' and resid 236 through 238'
    Processing helix  chain 'D' and resid 248 through 257
      Proline residue:  D 252  - end of helix
      removed outlier: 3.720A  pdb=" N   LEU D 256 " --> pdb=" O   LEU D 253 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 260 through 267
    Processing helix  chain 'D' and resid 270 through 272
      No H-bonds generated for 'chain 'D' and resid 270 through 272'
    Processing helix  chain 'D' and resid 277 through 299
    Processing helix  chain 'D' and resid 316 through 332
      removed outlier: 6.520A  pdb=" N   SER D 321 " --> pdb=" O   SER D 318 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU D 326 " --> pdb=" O   THR D 323 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   MET D 331 " --> pdb=" O   HIS D 328 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 344 through 347
    Processing helix  chain 'D' and resid 349 through 354
      removed outlier: 3.705A  pdb=" N   GLU D 353 " --> pdb=" O   PRO D 349 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   VAL D 354 " --> pdb=" O   GLU D 350 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 349 through 354'
    Processing helix  chain 'D' and resid 356 through 367
    Processing helix  chain 'D' and resid 383 through 396
    Processing helix  chain 'D' and resid 405 through 417
    Processing helix  chain 'D' and resid 470 through 472
      No H-bonds generated for 'chain 'D' and resid 470 through 472'
    Processing helix  chain 'D' and resid 474 through 479
    Processing helix  chain 'D' and resid 500 through 506
      removed outlier: 3.842A  pdb=" N   SER D 505 " --> pdb=" O   ASN D 501 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   ARG D 506 " --> pdb=" O   ASP D 502 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 538 through 541
      removed outlier: 3.571A  pdb=" N   THR D 541 " --> pdb=" O   PRO D 538 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 538 through 541'
    Processing helix  chain 'D' and resid 549 through 558
    Processing helix  chain 'D' and resid 562 through 570
    Processing helix  chain 'A' and resid 16 through 30
      removed outlier: 3.646A  pdb=" N   LEU A  30 " --> pdb=" O   LEU A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 78
    Processing helix  chain 'A' and resid 84 through 86
      No H-bonds generated for 'chain 'A' and resid 84 through 86'
    Processing helix  chain 'A' and resid 90 through 102
    Processing helix  chain 'A' and resid 113 through 130
      removed outlier: 7.026A  pdb=" N   THR A 118 " --> pdb=" O   VAL A 114 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LYS A 130 " --> pdb=" O   GLN A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 169
      removed outlier: 3.992A  pdb=" N   PHE A 168 " --> pdb=" O   ARG A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 174
      No H-bonds generated for 'chain 'A' and resid 172 through 174'
    Processing helix  chain 'A' and resid 193 through 205
    Processing helix  chain 'A' and resid 222 through 231
    Processing helix  chain 'A' and resid 236 through 238
      No H-bonds generated for 'chain 'A' and resid 236 through 238'
    Processing helix  chain 'A' and resid 248 through 257
      Proline residue:  A 252  - end of helix
      removed outlier: 3.720A  pdb=" N   LEU A 256 " --> pdb=" O   LEU A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 267
    Processing helix  chain 'A' and resid 270 through 272
      No H-bonds generated for 'chain 'A' and resid 270 through 272'
    Processing helix  chain 'A' and resid 277 through 299
    Processing helix  chain 'A' and resid 316 through 332
      removed outlier: 6.520A  pdb=" N   SER A 321 " --> pdb=" O   SER A 318 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU A 326 " --> pdb=" O   THR A 323 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   MET A 331 " --> pdb=" O   HIS A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 347
    Processing helix  chain 'A' and resid 349 through 354
      removed outlier: 3.705A  pdb=" N   GLU A 353 " --> pdb=" O   PRO A 349 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL A 354 " --> pdb=" O   GLU A 350 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 349 through 354'
    Processing helix  chain 'A' and resid 356 through 367
    Processing helix  chain 'A' and resid 383 through 396
    Processing helix  chain 'A' and resid 405 through 417
    Processing helix  chain 'A' and resid 470 through 472
      No H-bonds generated for 'chain 'A' and resid 470 through 472'
    Processing helix  chain 'A' and resid 474 through 479
    Processing helix  chain 'A' and resid 500 through 506
      removed outlier: 3.841A  pdb=" N   SER A 505 " --> pdb=" O   ASN A 501 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   ARG A 506 " --> pdb=" O   ASP A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 541
      removed outlier: 3.571A  pdb=" N   THR A 541 " --> pdb=" O   PRO A 538 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 538 through 541'
    Processing helix  chain 'A' and resid 549 through 558
    Processing helix  chain 'A' and resid 562 through 570
    Processing helix  chain 'B' and resid 16 through 30
      removed outlier: 3.646A  pdb=" N   LEU B  30 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 78
    Processing helix  chain 'B' and resid 84 through 86
      No H-bonds generated for 'chain 'B' and resid 84 through 86'
    Processing helix  chain 'B' and resid 90 through 102
    Processing helix  chain 'B' and resid 113 through 130
      removed outlier: 7.027A  pdb=" N   THR B 118 " --> pdb=" O   VAL B 114 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LYS B 130 " --> pdb=" O   GLN B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 169
      removed outlier: 3.991A  pdb=" N   PHE B 168 " --> pdb=" O   ARG B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 174
      No H-bonds generated for 'chain 'B' and resid 172 through 174'
    Processing helix  chain 'B' and resid 193 through 205
    Processing helix  chain 'B' and resid 222 through 231
    Processing helix  chain 'B' and resid 236 through 238
      No H-bonds generated for 'chain 'B' and resid 236 through 238'
    Processing helix  chain 'B' and resid 248 through 257
      Proline residue:  B 252  - end of helix
      removed outlier: 3.720A  pdb=" N   LEU B 256 " --> pdb=" O   LEU B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 267
    Processing helix  chain 'B' and resid 270 through 272
      No H-bonds generated for 'chain 'B' and resid 270 through 272'
    Processing helix  chain 'B' and resid 277 through 299
    Processing helix  chain 'B' and resid 316 through 332
      removed outlier: 6.520A  pdb=" N   SER B 321 " --> pdb=" O   SER B 318 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU B 326 " --> pdb=" O   THR B 323 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   MET B 331 " --> pdb=" O   HIS B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 347
    Processing helix  chain 'B' and resid 349 through 354
      removed outlier: 3.705A  pdb=" N   GLU B 353 " --> pdb=" O   PRO B 349 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   VAL B 354 " --> pdb=" O   GLU B 350 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 349 through 354'
    Processing helix  chain 'B' and resid 356 through 367
    Processing helix  chain 'B' and resid 383 through 396
    Processing helix  chain 'B' and resid 405 through 417
    Processing helix  chain 'B' and resid 470 through 472
      No H-bonds generated for 'chain 'B' and resid 470 through 472'
    Processing helix  chain 'B' and resid 474 through 479
    Processing helix  chain 'B' and resid 500 through 506
      removed outlier: 3.841A  pdb=" N   SER B 505 " --> pdb=" O   ASN B 501 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   ARG B 506 " --> pdb=" O   ASP B 502 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 541
      removed outlier: 3.571A  pdb=" N   THR B 541 " --> pdb=" O   PRO B 538 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 538 through 541'
    Processing helix  chain 'B' and resid 549 through 558
    Processing helix  chain 'B' and resid 562 through 570
    Processing helix  chain 'C' and resid 16 through 30
      removed outlier: 3.646A  pdb=" N   LEU C  30 " --> pdb=" O   LEU C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 78
    Processing helix  chain 'C' and resid 84 through 86
      No H-bonds generated for 'chain 'C' and resid 84 through 86'
    Processing helix  chain 'C' and resid 90 through 102
    Processing helix  chain 'C' and resid 116 through 130
      removed outlier: 3.692A  pdb=" N   LYS C 130 " --> pdb=" O   GLN C 126 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 157 through 169
      removed outlier: 3.992A  pdb=" N   PHE C 168 " --> pdb=" O   ARG C 164 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 174
      No H-bonds generated for 'chain 'C' and resid 172 through 174'
    Processing helix  chain 'C' and resid 193 through 205
    Processing helix  chain 'C' and resid 222 through 231
    Processing helix  chain 'C' and resid 236 through 238
      No H-bonds generated for 'chain 'C' and resid 236 through 238'
    Processing helix  chain 'C' and resid 248 through 257
      Proline residue:  C 252  - end of helix
      removed outlier: 3.720A  pdb=" N   LEU C 256 " --> pdb=" O   LEU C 253 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 260 through 267
    Processing helix  chain 'C' and resid 270 through 272
      No H-bonds generated for 'chain 'C' and resid 270 through 272'
    Processing helix  chain 'C' and resid 277 through 299
    Processing helix  chain 'C' and resid 316 through 332
      removed outlier: 6.520A  pdb=" N   SER C 321 " --> pdb=" O   SER C 318 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU C 326 " --> pdb=" O   THR C 323 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   MET C 331 " --> pdb=" O   HIS C 328 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 344 through 347
    Processing helix  chain 'C' and resid 349 through 354
      removed outlier: 3.705A  pdb=" N   GLU C 353 " --> pdb=" O   PRO C 349 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   VAL C 354 " --> pdb=" O   GLU C 350 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 349 through 354'
    Processing helix  chain 'C' and resid 356 through 367
    Processing helix  chain 'C' and resid 383 through 396
    Processing helix  chain 'C' and resid 405 through 417
    Processing helix  chain 'C' and resid 470 through 472
      No H-bonds generated for 'chain 'C' and resid 470 through 472'
    Processing helix  chain 'C' and resid 474 through 479
    Processing helix  chain 'C' and resid 500 through 506
      removed outlier: 3.841A  pdb=" N   SER C 505 " --> pdb=" O   ASN C 501 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   ARG C 506 " --> pdb=" O   ASP C 502 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 538 through 541
      removed outlier: 3.571A  pdb=" N   THR C 541 " --> pdb=" O   PRO C 538 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 538 through 541'
    Processing helix  chain 'C' and resid 549 through 558
    Processing helix  chain 'C' and resid 562 through 570
    Processing sheet with id=  A, first strand: chain 'D' and resid 239 through 242
      removed outlier: 6.568A  pdb=" N   ILE D 212 " --> pdb=" O   VAL D 240 " (cutoff:3.500A)
      removed outlier: 7.597A  pdb=" N   VAL D 242 " --> pdb=" O   ILE D 212 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   CYS D 214 " --> pdb=" O   VAL D 242 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   TYR D   3 " --> pdb=" O   ALA D 176 " (cutoff:3.500A)
      removed outlier: 7.522A  pdb=" N   ILE D 178 " --> pdb=" O   TYR D   3 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   VAL D   5 " --> pdb=" O   ILE D 178 " (cutoff:3.500A)
      removed outlier: 7.349A  pdb=" N   VAL D 180 " --> pdb=" O   VAL D   5 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   SER D   7 " --> pdb=" O   VAL D 180 " (cutoff:3.500A)
      removed outlier: 8.634A  pdb=" N   LEU D 182 " --> pdb=" O   SER D   7 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'D' and resid 58 through 60
    Processing sheet with id=  C, first strand: chain 'D' and resid 336 through 343
      removed outlier: 6.763A  pdb=" N   GLY D 371 " --> pdb=" O   ALA D 307 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   VAL D 309 " --> pdb=" O   GLY D 371 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   LEU D 373 " --> pdb=" O   VAL D 309 " (cutoff:3.500A)
      removed outlier: 7.834A  pdb=" N   VAL D 374 " --> pdb=" O   PRO D 399 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   LEU D 401 " --> pdb=" O   VAL D 374 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'D' and resid 440 through 442
    Processing sheet with id=  E, first strand: chain 'D' and resid 458 through 465
    Processing sheet with id=  F, first strand: chain 'A' and resid 239 through 242
      removed outlier: 6.568A  pdb=" N   ILE A 212 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
      removed outlier: 7.597A  pdb=" N   VAL A 242 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   CYS A 214 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   TYR A   3 " --> pdb=" O   ALA A 176 " (cutoff:3.500A)
      removed outlier: 7.522A  pdb=" N   ILE A 178 " --> pdb=" O   TYR A   3 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   VAL A   5 " --> pdb=" O   ILE A 178 " (cutoff:3.500A)
      removed outlier: 7.349A  pdb=" N   VAL A 180 " --> pdb=" O   VAL A   5 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   SER A   7 " --> pdb=" O   VAL A 180 " (cutoff:3.500A)
      removed outlier: 8.633A  pdb=" N   LEU A 182 " --> pdb=" O   SER A   7 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'A' and resid 58 through 60
    Processing sheet with id=  H, first strand: chain 'A' and resid 336 through 343
      removed outlier: 6.762A  pdb=" N   GLY A 371 " --> pdb=" O   ALA A 307 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   VAL A 309 " --> pdb=" O   GLY A 371 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   LEU A 373 " --> pdb=" O   VAL A 309 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   VAL A 374 " --> pdb=" O   PRO A 399 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   LEU A 401 " --> pdb=" O   VAL A 374 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'A' and resid 440 through 442
    Processing sheet with id=  J, first strand: chain 'A' and resid 458 through 465
    Processing sheet with id=  K, first strand: chain 'B' and resid 239 through 242
      removed outlier: 6.568A  pdb=" N   ILE B 212 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
      removed outlier: 7.596A  pdb=" N   VAL B 242 " --> pdb=" O   ILE B 212 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   CYS B 214 " --> pdb=" O   VAL B 242 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   TYR B   3 " --> pdb=" O   ALA B 176 " (cutoff:3.500A)
      removed outlier: 7.522A  pdb=" N   ILE B 178 " --> pdb=" O   TYR B   3 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   VAL B   5 " --> pdb=" O   ILE B 178 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   VAL B 180 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   SER B   7 " --> pdb=" O   VAL B 180 " (cutoff:3.500A)
      removed outlier: 8.633A  pdb=" N   LEU B 182 " --> pdb=" O   SER B   7 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'B' and resid 58 through 60
    Processing sheet with id=  M, first strand: chain 'B' and resid 336 through 343
      removed outlier: 6.763A  pdb=" N   GLY B 371 " --> pdb=" O   ALA B 307 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   VAL B 309 " --> pdb=" O   GLY B 371 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   LEU B 373 " --> pdb=" O   VAL B 309 " (cutoff:3.500A)
      removed outlier: 7.834A  pdb=" N   VAL B 374 " --> pdb=" O   PRO B 399 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   LEU B 401 " --> pdb=" O   VAL B 374 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'B' and resid 440 through 442
    Processing sheet with id=  O, first strand: chain 'B' and resid 458 through 465
    Processing sheet with id=  P, first strand: chain 'C' and resid 239 through 242
      removed outlier: 6.567A  pdb=" N   ILE C 212 " --> pdb=" O   VAL C 240 " (cutoff:3.500A)
      removed outlier: 7.596A  pdb=" N   VAL C 242 " --> pdb=" O   ILE C 212 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   CYS C 214 " --> pdb=" O   VAL C 242 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   TYR C   3 " --> pdb=" O   ALA C 176 " (cutoff:3.500A)
      removed outlier: 7.522A  pdb=" N   ILE C 178 " --> pdb=" O   TYR C   3 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   VAL C   5 " --> pdb=" O   ILE C 178 " (cutoff:3.500A)
      removed outlier: 7.349A  pdb=" N   VAL C 180 " --> pdb=" O   VAL C   5 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   SER C   7 " --> pdb=" O   VAL C 180 " (cutoff:3.500A)
      removed outlier: 8.634A  pdb=" N   LEU C 182 " --> pdb=" O   SER C   7 " (cutoff:3.500A)
    Processing sheet with id=  Q, first strand: chain 'C' and resid 58 through 60
    Processing sheet with id=  R, first strand: chain 'C' and resid 336 through 343
      removed outlier: 6.763A  pdb=" N   GLY C 371 " --> pdb=" O   ALA C 307 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   VAL C 309 " --> pdb=" O   GLY C 371 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   LEU C 373 " --> pdb=" O   VAL C 309 " (cutoff:3.500A)
      removed outlier: 7.834A  pdb=" N   VAL C 374 " --> pdb=" O   PRO C 399 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   LEU C 401 " --> pdb=" O   VAL C 374 " (cutoff:3.500A)
    Processing sheet with id=  S, first strand: chain 'C' and resid 440 through 442
    Processing sheet with id=  T, first strand: chain 'C' and resid 458 through 465

    716 hydrogen bonds defined for protein.
    1944 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: 14.90

  Time building geometry restraints manager: 30.68 seconds

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

  Histogram of bond lengths:
        0.93 -     1.10: 17532
        1.10 -     1.28: 3012
        1.28 -     1.46: 5638
        1.46 -     1.64: 9390
        1.64 -     1.82: 128
  Bond restraints: 35700
  Sorted by residual:
  bond pdb=" C2' UTP B 602 "
       pdb=" C3' UTP B 602 "
    ideal  model  delta    sigma   weight residual
    1.301  1.540 -0.239 2.00e-02 2.50e+03 1.42e+02
  bond pdb=" C2' UTP C 602 "
       pdb=" C3' UTP C 602 "
    ideal  model  delta    sigma   weight residual
    1.301  1.539 -0.238 2.00e-02 2.50e+03 1.42e+02
  bond pdb=" C2' UTP D 601 "
       pdb=" C3' UTP D 601 "
    ideal  model  delta    sigma   weight residual
    1.301  1.539 -0.238 2.00e-02 2.50e+03 1.42e+02
  bond pdb=" C2' UTP A 601 "
       pdb=" C3' UTP A 601 "
    ideal  model  delta    sigma   weight residual
    1.301  1.539 -0.238 2.00e-02 2.50e+03 1.41e+02
  bond pdb=" C1' UTP B 602 "
       pdb=" N1  UTP B 602 "
    ideal  model  delta    sigma   weight residual
    1.305  1.487 -0.182 2.00e-02 2.50e+03 8.26e+01
  ... (remaining 35695 not shown)

  Histogram of bond angle deviations from ideal:
       77.84 -    92.00: 12
       92.00 -   106.16: 1489
      106.16 -   120.31: 54878
      120.31 -   134.47: 8249
      134.47 -   148.62: 24
  Bond angle restraints: 64652
  Sorted by residual:
  angle pdb=" N   SER A 217 "
        pdb=" CA  SER A 217 "
        pdb=" HA  SER A 217 "
      ideal   model   delta    sigma   weight residual
     110.00   78.10   31.90 3.00e+00 1.11e-01 1.13e+02
  angle pdb=" N   SER C 217 "
        pdb=" CA  SER C 217 "
        pdb=" HA  SER C 217 "
      ideal   model   delta    sigma   weight residual
     110.00   78.13   31.87 3.00e+00 1.11e-01 1.13e+02
  angle pdb=" N   SER B 217 "
        pdb=" CA  SER B 217 "
        pdb=" HA  SER B 217 "
      ideal   model   delta    sigma   weight residual
     110.00   78.14   31.86 3.00e+00 1.11e-01 1.13e+02
  angle pdb=" N   SER D 217 "
        pdb=" CA  SER D 217 "
        pdb=" HA  SER D 217 "
      ideal   model   delta    sigma   weight residual
     110.00   78.14   31.86 3.00e+00 1.11e-01 1.13e+02
  angle pdb=" C   SER A 217 "
        pdb=" CA  SER A 217 "
        pdb=" HA  SER A 217 "
      ideal   model   delta    sigma   weight residual
     109.00   77.84   31.16 3.00e+00 1.11e-01 1.08e+02
  ... (remaining 64647 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 14791
       17.80 -    35.61: 1159
       35.61 -    53.41: 418
       53.41 -    71.21: 292
       71.21 -    89.02: 40
  Dihedral angle restraints: 16700
    sinusoidal: 9352
      harmonic: 7348
  Sorted by residual:
  dihedral pdb=" C   SER C 217 "
           pdb=" N   SER C 217 "
           pdb=" CA  SER C 217 "
           pdb=" CB  SER C 217 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -144.12   21.52     0      2.50e+00 1.60e-01 7.41e+01
  dihedral pdb=" C   SER B 217 "
           pdb=" N   SER B 217 "
           pdb=" CA  SER B 217 "
           pdb=" CB  SER B 217 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -144.12   21.52     0      2.50e+00 1.60e-01 7.41e+01
  dihedral pdb=" C   SER D 217 "
           pdb=" N   SER D 217 "
           pdb=" CA  SER D 217 "
           pdb=" CB  SER D 217 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -144.07   21.47     0      2.50e+00 1.60e-01 7.37e+01
  ... (remaining 16697 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.188: 2584
       0.188 -    0.375: 192
       0.375 -    0.563: 4
       0.563 -    0.750: 0
       0.750 -    0.938: 4
  Chirality restraints: 2784
  Sorted by residual:
  chirality pdb=" CA  SER C 217 "
            pdb=" N   SER C 217 "
            pdb=" C   SER C 217 "
            pdb=" CB  SER C 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.57    0.94 2.00e-01 2.50e+01 2.20e+01
  chirality pdb=" CA  SER B 217 "
            pdb=" N   SER B 217 "
            pdb=" C   SER B 217 "
            pdb=" CB  SER B 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.57    0.94 2.00e-01 2.50e+01 2.20e+01
  chirality pdb=" CA  SER D 217 "
            pdb=" N   SER D 217 "
            pdb=" C   SER D 217 "
            pdb=" CB  SER D 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.58    0.93 2.00e-01 2.50e+01 2.18e+01
  ... (remaining 2781 not shown)

  Planarity restraints: 5260
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 488 "    0.145 9.50e-02 1.11e+02   1.05e-01 1.96e+02
        pdb=" NE  ARG B 488 "    0.067 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 488 "    0.076 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 488 "    0.064 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 488 "    0.054 2.00e-02 2.50e+03
        pdb="HH11 ARG B 488 "   -0.190 2.00e-02 2.50e+03
        pdb="HH12 ARG B 488 "    0.080 2.00e-02 2.50e+03
        pdb="HH21 ARG B 488 "   -0.131 2.00e-02 2.50e+03
        pdb="HH22 ARG B 488 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 488 "    0.145 9.50e-02 1.11e+02   1.05e-01 1.96e+02
        pdb=" NE  ARG A 488 "    0.067 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 488 "    0.075 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 488 "    0.065 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 488 "    0.054 2.00e-02 2.50e+03
        pdb="HH11 ARG A 488 "   -0.190 2.00e-02 2.50e+03
        pdb="HH12 ARG A 488 "    0.079 2.00e-02 2.50e+03
        pdb="HH21 ARG A 488 "   -0.131 2.00e-02 2.50e+03
        pdb="HH22 ARG A 488 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 488 "   -0.145 9.50e-02 1.11e+02   1.05e-01 1.96e+02
        pdb=" NE  ARG D 488 "   -0.067 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 488 "   -0.075 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 488 "   -0.064 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 488 "   -0.054 2.00e-02 2.50e+03
        pdb="HH11 ARG D 488 "    0.190 2.00e-02 2.50e+03
        pdb="HH12 ARG D 488 "   -0.079 2.00e-02 2.50e+03
        pdb="HH21 ARG D 488 "    0.131 2.00e-02 2.50e+03
        pdb="HH22 ARG D 488 "    0.024 2.00e-02 2.50e+03
  ... (remaining 5257 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.12: 1818
        2.12 -     2.74: 56993
        2.74 -     3.36: 107231
        3.36 -     3.98: 144250
        3.98 -     4.60: 212132
  Nonbonded interactions: 522424
  Sorted by model distance:
  nonbonded pdb=" HE1 HIS D 233 "
            pdb="HE21 GLN A 165 "
     model   vdw
     1.506 2.100
  nonbonded pdb=" HE1 HIS B 233 "
            pdb="HE21 GLN C 165 "
     model   vdw
     1.508 2.100
  nonbonded pdb="HE21 GLN D 165 "
            pdb=" HE1 HIS A 233 "
     model   vdw
     1.510 2.100
  nonbonded pdb="HE21 GLN B 165 "
            pdb=" HE1 HIS C 233 "
     model   vdw
     1.536 2.100
  nonbonded pdb=" H   LYS A 193 "
            pdb=" O3G UTP B 602 "
     model   vdw
     1.555 1.850
  ... (remaining 522419 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' and (resid 1 through 571 or resid 604))
  selection = (chain 'B' and (resid 1 through 571 or resid 604))
  selection = (chain 'C' and (resid 1 through 571 or resid 604))
  selection = (chain 'D' and (resid 1 through 571 or resid 604))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.240
  Construct map_model_manager:             0.530
  Extract box with map and model:          8.610
  Check model and map are aligned:         0.510
  Set scattering table:                    0.300
  Process input model:                     113.630
  Find NCS groups from input model:        1.910
  Set up NCS constraints:                  0.150
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:10.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  137.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
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      :  0.014   0.239  18136  Z= 0.955
  Angle     :  1.979  15.312  24620  Z= 1.303
  Chirality :  0.108   0.938   2784
  Planarity :  0.015   0.128   3132
  Dihedral  : 15.270  89.018   6848
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 0.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  6.15 %
    Favored  : 92.21 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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: -0.45 (0.17), residues: 2220
  helix: -0.44 (0.15), residues: 936
  sheet:  0.06 (0.26), residues: 332
  loop : -0.05 (0.21), residues: 952

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.108   0.028   TRP A 472 
 HIS   0.029   0.006   HIS B 179 
 PHE   0.077   0.015   PHE B 168 
 TYR   0.080   0.021   TYR A  74 
 ARG   0.014   0.002   ARG B 215 

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

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

  4440 Ramachandran restraints generated.
    2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4440 Ramachandran restraints generated.
    2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Evaluate side-chains
  463 residues out of total 1952 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 431
  time to evaluate  : 2.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  103 ARG cc_start: 0.7699 (ttp-110) cc_final: 0.7275 (mtm-85)
REVERT: D  105 ASP cc_start: 0.7432 (m-30) cc_final: 0.7069 (m-30)
REVERT: D  146 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7728 (tt0)
REVERT: D  165 GLN cc_start: 0.8479 (mt0) cc_final: 0.8108 (mt0)
REVERT: D  201 ASP cc_start: 0.7703 (m-30) cc_final: 0.7475 (m-30)
REVERT: D  241 ASN cc_start: 0.8109 (t0) cc_final: 0.7861 (t0)
REVERT: D  287 LEU cc_start: 0.7839 (tp) cc_final: 0.7553 (tm)
REVERT: D  443 ILE cc_start: 0.6597 (OUTLIER) cc_final: 0.6352 (tp)
REVERT: D  548 SER cc_start: 0.8545 (t) cc_final: 0.8258 (t)
REVERT: A  103 ARG cc_start: 0.7668 (ttp-110) cc_final: 0.7298 (mtm-85)
REVERT: A  105 ASP cc_start: 0.7327 (m-30) cc_final: 0.7126 (m-30)
REVERT: A  146 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7683 (tt0)
REVERT: A  165 GLN cc_start: 0.8474 (mt0) cc_final: 0.8106 (mt0)
REVERT: A  201 ASP cc_start: 0.7699 (m-30) cc_final: 0.7474 (m-30)
REVERT: A  257 LYS cc_start: 0.7980 (ptmm) cc_final: 0.7737 (ptmm)
REVERT: A  443 ILE cc_start: 0.6637 (OUTLIER) cc_final: 0.6361 (tp)
REVERT: B  103 ARG cc_start: 0.7713 (ttp-110) cc_final: 0.7332 (mtm-85)
REVERT: B  105 ASP cc_start: 0.7369 (m-30) cc_final: 0.7026 (m-30)
REVERT: B  146 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7715 (tt0)
REVERT: B  165 GLN cc_start: 0.8460 (mt0) cc_final: 0.8084 (mt0)
REVERT: B  201 ASP cc_start: 0.7666 (m-30) cc_final: 0.7446 (m-30)
REVERT: B  241 ASN cc_start: 0.8088 (t0) cc_final: 0.7860 (t0)
REVERT: B  287 LEU cc_start: 0.7838 (tp) cc_final: 0.7554 (tm)
REVERT: B  443 ILE cc_start: 0.6641 (OUTLIER) cc_final: 0.6392 (tp)
REVERT: C  103 ARG cc_start: 0.7663 (ttp-110) cc_final: 0.7250 (mtm-85)
REVERT: C  105 ASP cc_start: 0.7461 (m-30) cc_final: 0.7118 (m-30)
REVERT: C  146 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7734 (tt0)
REVERT: C  165 GLN cc_start: 0.8479 (mt0) cc_final: 0.8250 (mt0)
REVERT: C  201 ASP cc_start: 0.7698 (m-30) cc_final: 0.7488 (m-30)
REVERT: C  222 ARG cc_start: 0.7229 (mmt180) cc_final: 0.7001 (tpp-160)
REVERT: C  241 ASN cc_start: 0.8077 (t0) cc_final: 0.7852 (t0)
REVERT: C  287 LEU cc_start: 0.7843 (tp) cc_final: 0.7534 (tm)
REVERT: C  443 ILE cc_start: 0.6603 (OUTLIER) cc_final: 0.6337 (tp)
  outliers start: 32
  outliers final: 4
  residues processed: 455
  average time/residue: 2.5242
  time to fit residues: 1303.5067
Evaluate side-chains
  338 residues out of total 1952 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 326
  time to evaluate  : 2.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  146 GLU
Chi-restraints excluded: chain D residue  443 ILE
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  146 GLU
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  146 GLU
Chi-restraints excluded: chain B residue  443 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  146 GLU
Chi-restraints excluded: chain C residue  443 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 185 optimal weight:    0.6980
   chunk 166 optimal weight:    0.6980
   chunk 92 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 112 optimal weight:    0.7980
   chunk 89 optimal weight:    0.8980
   chunk 172 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 104 optimal weight:    5.9990
   chunk 128 optimal weight:    0.9980
   chunk 199 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
D 116 HIS
D 167 GLN
D 285 GLN
A 116 HIS
A 285 GLN
B 116 HIS
C 116 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.2939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  18136  Z= 0.219
  Angle     :  0.604   7.245  24620  Z= 0.316
  Chirality :  0.047   0.388   2784
  Planarity :  0.005   0.050   3132
  Dihedral  :  9.945  72.205   2604
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 12.45 %
    Favored  : 85.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.33 (0.18), residues: 2220
  helix:  0.62 (0.16), residues: 968
  sheet:  0.32 (0.26), residues: 332
  loop : -0.09 (0.21), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 290 
 HIS   0.008   0.002   HIS A 116 
 PHE   0.008   0.002   PHE D 400 
 TYR   0.015   0.002   TYR B 312 
 ARG   0.007   0.001   ARG A 334 

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

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

  4440 Ramachandran restraints generated.
    2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4440 Ramachandran restraints generated.
    2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Evaluate side-chains
  409 residues out of total 1952 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 360
  time to evaluate  : 2.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  201 ASP cc_start: 0.7449 (m-30) cc_final: 0.7209 (m-30)
REVERT: D  222 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7313 (tpp-160)
REVERT: D  248 THR cc_start: 0.8584 (p) cc_final: 0.8289 (m)
REVERT: D  272 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6970 (mt-10)
REVERT: D  338 GLU cc_start: 0.7325 (tt0) cc_final: 0.7104 (tt0)
REVERT: D  443 ILE cc_start: 0.6581 (OUTLIER) cc_final: 0.6363 (tp)
REVERT: A  201 ASP cc_start: 0.7400 (m-30) cc_final: 0.7159 (m-30)
REVERT: A  222 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7285 (tpp-160)
REVERT: A  272 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6949 (mt-10)
REVERT: A  338 GLU cc_start: 0.7373 (tt0) cc_final: 0.7115 (tt0)
REVERT: A  443 ILE cc_start: 0.6574 (OUTLIER) cc_final: 0.6344 (tp)
REVERT: B   75 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8088 (mt-10)
REVERT: B  189 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7577 (tp30)
REVERT: B  201 ASP cc_start: 0.7376 (m-30) cc_final: 0.7130 (m-30)
REVERT: B  248 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8315 (m)
REVERT: B  272 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6983 (mt-10)
REVERT: B  338 GLU cc_start: 0.7361 (tt0) cc_final: 0.7089 (tt0)
REVERT: B  443 ILE cc_start: 0.6650 (OUTLIER) cc_final: 0.6450 (tp)
REVERT: C  201 ASP cc_start: 0.7393 (m-30) cc_final: 0.7143 (m-30)
REVERT: C  248 THR cc_start: 0.8583 (p) cc_final: 0.8322 (m)
REVERT: C  272 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6987 (mt-10)
REVERT: C  338 GLU cc_start: 0.7465 (tt0) cc_final: 0.7166 (tt0)
REVERT: C  443 ILE cc_start: 0.6604 (OUTLIER) cc_final: 0.6363 (tp)
  outliers start: 49
  outliers final: 20
  residues processed: 394
  average time/residue: 2.2837
  time to fit residues: 1034.7618
Evaluate side-chains
  352 residues out of total 1952 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 324
  time to evaluate  : 2.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   12 SER
Chi-restraints excluded: chain D residue   42 TYR
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  222 ARG
Chi-restraints excluded: chain D residue  321 SER
Chi-restraints excluded: chain D residue  443 ILE
Chi-restraints excluded: chain D residue  490 ARG
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain A residue   42 TYR
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  222 ARG
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  490 ARG
Chi-restraints excluded: chain B residue   12 SER
Chi-restraints excluded: chain B residue   42 TYR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  189 GLU
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  443 ILE
Chi-restraints excluded: chain B residue  490 ARG
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  321 SER
Chi-restraints excluded: chain C residue  443 ILE
Chi-restraints excluded: chain C residue  490 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 111 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 166 optimal weight:    0.9990
   chunk 136 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 200 optimal weight:    0.9990
   chunk 216 optimal weight:    3.9990
   chunk 178 optimal weight:    0.0370
   chunk 198 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0970
   chunk 160 optimal weight:    5.9990
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
D 165 GLN
D 285 GLN
A 165 GLN
A 196 GLN
B 165 GLN
C 165 GLN
C 196 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.3564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  18136  Z= 0.171
  Angle     :  0.518   4.762  24620  Z= 0.270
  Chirality :  0.046   0.378   2784
  Planarity :  0.004   0.078   3132
  Dihedral  :  9.040  67.735   2588
  Min Nonbonded Distance : 1.823

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 13.42 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.58 (0.18), residues: 2220
  helix:  1.02 (0.17), residues: 972
  sheet:  0.18 (0.26), residues: 336
  loop : -0.08 (0.21), residues: 912

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 124 
 HIS   0.006   0.001   HIS B 233 
 PHE   0.011   0.002   PHE A 508 
 TYR   0.013   0.001   TYR C  42 
 ARG   0.007   0.000   ARG B 334 

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

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

  4440 Ramachandran restraints generated.
    2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4440 Ramachandran restraints generated.
    2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Evaluate side-chains
  402 residues out of total 1952 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 56
    poor density    : 346
  time to evaluate  : 2.863 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  201 ASP cc_start: 0.7404 (m-30) cc_final: 0.7148 (m-30)
REVERT: D  222 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7193 (tpp-160)
REVERT: D  338 GLU cc_start: 0.7449 (tt0) cc_final: 0.7156 (tt0)
REVERT: A  201 ASP cc_start: 0.7435 (m-30) cc_final: 0.7204 (m-30)
REVERT: A  222 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7137 (tpp-160)
REVERT: A  291 GLU cc_start: 0.7239 (mt-10) cc_final: 0.7005 (mm-30)
REVERT: A  486 HIS cc_start: 0.7810 (m90) cc_final: 0.7585 (m90)
REVERT: B  201 ASP cc_start: 0.7390 (m-30) cc_final: 0.7150 (m-30)
REVERT: B  219 GLU cc_start: 0.7313 (tp30) cc_final: 0.6975 (tp30)
REVERT: B  241 ASN cc_start: 0.8286 (t0) cc_final: 0.7952 (t0)
REVERT: B  248 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8376 (m)
REVERT: B  338 GLU cc_start: 0.7419 (tt0) cc_final: 0.7139 (tt0)
REVERT: C  201 ASP cc_start: 0.7412 (m-30) cc_final: 0.7186 (m-30)
REVERT: C  272 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6977 (mt-10)
  outliers start: 56
  outliers final: 18
  residues processed: 379
  average time/residue: 2.1889
  time to fit residues: 970.1260
Evaluate side-chains
  334 residues out of total 1952 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 313
  time to evaluate  : 3.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   12 SER
Chi-restraints excluded: chain D residue   42 TYR
Chi-restraints excluded: chain D residue   57 GLU
Chi-restraints excluded: chain D residue  222 ARG
Chi-restraints excluded: chain D residue  321 SER
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain A residue   42 TYR
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  222 ARG
Chi-restraints excluded: chain B residue   12 SER
Chi-restraints excluded: chain B residue   42 TYR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  539 GLU
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  321 SER
Chi-restraints excluded: chain C residue  539 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 197 optimal weight:    0.9980
   chunk 150 optimal weight:    2.9990
   chunk 103 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 134 optimal weight:    0.9980
   chunk 200 optimal weight:    4.9990
   chunk 212 optimal weight:    2.9990
   chunk 104 optimal weight:    3.9990
   chunk 190 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
D 285 GLN
D 535 GLN
A 285 GLN
B 535 GLN
C 535 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.3875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  18136  Z= 0.229
  Angle     :  0.522   4.479  24620  Z= 0.271
  Chirality :  0.046   0.380   2784
  Planarity :  0.005   0.080   3132
  Dihedral  :  8.910  65.354   2580
  Min Nonbonded Distance : 1.833

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.65 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.58 (0.18), residues: 2220
  helix:  1.07 (0.17), residues: 968
  sheet:  0.22 (0.26), residues: 328
  loop : -0.18 (0.20), residues: 924

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 124 
 HIS   0.006   0.001   HIS A 233 
 PHE   0.012   0.002   PHE A 175 
 TYR   0.016   0.001   TYR C  42 
 ARG   0.009   0.001   ARG A 476 

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

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

  4440 Ramachandran restraints generated.
    2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4440 Ramachandran restraints generated.
    2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Evaluate side-chains
  356 residues out of total 1952 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 308
  time to evaluate  : 2.885 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  201 ASP cc_start: 0.7445 (m-30) cc_final: 0.7169 (m-30)
REVERT: D  222 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7261 (tpp-160)
REVERT: A   75 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8165 (mt-10)
REVERT: A  201 ASP cc_start: 0.7500 (m-30) cc_final: 0.7224 (m-30)
REVERT: A  222 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7191 (tpp-160)
REVERT: B  201 ASP cc_start: 0.7437 (m-30) cc_final: 0.7180 (m-30)
REVERT: B  219 GLU cc_start: 0.7385 (tp30) cc_final: 0.6978 (tp30)
REVERT: B  248 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8400 (m)
REVERT: C   75 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8159 (mt-10)
REVERT: C  201 ASP cc_start: 0.7504 (m-30) cc_final: 0.7232 (m-30)
REVERT: C  272 GLU cc_start: 0.7229 (mt-10) cc_final: 0.7008 (mt-10)
  outliers start: 48
  outliers final: 24
  residues processed: 344
  average time/residue: 2.1489
  time to fit residues: 857.9618
Evaluate side-chains
  327 residues out of total 1952 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 300
  time to evaluate  : 2.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   12 SER
Chi-restraints excluded: chain D residue   42 TYR
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  222 ARG
Chi-restraints excluded: chain D residue  321 SER
Chi-restraints excluded: chain D residue  539 GLU
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue   42 TYR
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue  222 ARG
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain B residue   12 SER
Chi-restraints excluded: chain B residue   25 MET
Chi-restraints excluded: chain B residue   42 TYR
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  539 GLU
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   25 MET
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  321 SER
Chi-restraints excluded: chain C residue  539 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 177 optimal weight:    1.9990
   chunk 120 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 158 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   chunk 181 optimal weight:    0.7980
   chunk 146 optimal weight:    5.9990
   chunk 0 optimal weight:    1.9990
   chunk 108 optimal weight:    0.7980
   chunk 190 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
D 285 GLN
D 535 GLN
A 285 GLN
B 535 GLN
C 535 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.4052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  18136  Z= 0.209
  Angle     :  0.502   4.889  24620  Z= 0.259
  Chirality :  0.046   0.376   2784
  Planarity :  0.005   0.077   3132
  Dihedral  :  8.708  62.527   2580
  Min Nonbonded Distance : 1.831

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 15.52 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.65 (0.18), residues: 2220
  helix:  1.10 (0.17), residues: 964
  sheet:  0.15 (0.27), residues: 328
  loop : -0.04 (0.21), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 124 
 HIS   0.005   0.001   HIS B 233 
 PHE   0.012   0.002   PHE B 523 
 TYR   0.018   0.002   TYR A 312 
 ARG   0.011   0.001   ARG A 476 

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

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

  4440 Ramachandran restraints generated.
    2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4440 Ramachandran restraints generated.
    2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Evaluate side-chains
  358 residues out of total 1952 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 309
  time to evaluate  : 2.958 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   28 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8106 (mtpp)
REVERT: D  130 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8334 (mtpm)
REVERT: D  195 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8265 (m)
REVERT: D  201 ASP cc_start: 0.7417 (m-30) cc_final: 0.7151 (m-30)
REVERT: D  222 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7265 (tpp-160)
REVERT: A   75 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8192 (mt-10)
REVERT: A  195 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8256 (m)
REVERT: A  200 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7470 (ttpp)
REVERT: A  201 ASP cc_start: 0.7453 (m-30) cc_final: 0.7167 (m-30)
REVERT: A  222 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7205 (tpp-160)
REVERT: A  272 GLU cc_start: 0.7235 (mt-10) cc_final: 0.7035 (mt-10)
REVERT: A  291 GLU cc_start: 0.7276 (mt-10) cc_final: 0.7060 (mm-30)
REVERT: B   28 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8115 (mtpp)
REVERT: B  130 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8324 (mtpm)
REVERT: B  195 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8265 (m)
REVERT: B  201 ASP cc_start: 0.7408 (m-30) cc_final: 0.7158 (m-30)
REVERT: B  219 GLU cc_start: 0.7322 (tp30) cc_final: 0.6931 (tp30)
REVERT: C   28 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8099 (mtpp)
REVERT: C   75 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8181 (mt-10)
REVERT: C  130 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8343 (mtpm)
REVERT: C  195 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8253 (m)
REVERT: C  200 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7488 (ttpp)
REVERT: C  201 ASP cc_start: 0.7466 (m-30) cc_final: 0.7183 (m-30)
REVERT: C  272 GLU cc_start: 0.7225 (mt-10) cc_final: 0.7019 (mt-10)
  outliers start: 49
  outliers final: 21
  residues processed: 347
  average time/residue: 2.2425
  time to fit residues: 897.1809
Evaluate side-chains
  323 residues out of total 1952 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 288
  time to evaluate  : 2.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   12 SER
Chi-restraints excluded: chain D residue   25 MET
Chi-restraints excluded: chain D residue   28 LYS
Chi-restraints excluded: chain D residue   42 TYR
Chi-restraints excluded: chain D residue  130 LYS
Chi-restraints excluded: chain D residue  195 THR
Chi-restraints excluded: chain D residue  222 ARG
Chi-restraints excluded: chain D residue  321 SER
Chi-restraints excluded: chain D residue  539 GLU
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain A residue   42 TYR
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  200 LYS
Chi-restraints excluded: chain A residue  222 ARG
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain B residue   12 SER
Chi-restraints excluded: chain B residue   28 LYS
Chi-restraints excluded: chain B residue   42 TYR
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue  130 LYS
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  539 GLU
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   28 LYS
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  130 LYS
Chi-restraints excluded: chain C residue  195 THR
Chi-restraints excluded: chain C residue  200 LYS
Chi-restraints excluded: chain C residue  321 SER
Chi-restraints excluded: chain C residue  539 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 71 optimal weight:    0.5980
   chunk 191 optimal weight:    1.9990
   chunk 42 optimal weight:    7.9990
   chunk 124 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 212 optimal weight:    0.9980
   chunk 176 optimal weight:    0.9980
   chunk 98 optimal weight:    8.9990
   chunk 17 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0870
   chunk 111 optimal weight:    0.9990
   overall best weight:    0.7358

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

Flipped N/Q/H residues before XYZ refinement:
D 196 GLN
D 535 GLN
A 535 GLN
B 196 GLN
C 535 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.4187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021  18136  Z= 0.193
  Angle     :  0.491   4.370  24620  Z= 0.254
  Chirality :  0.045   0.377   2784
  Planarity :  0.005   0.080   3132
  Dihedral  :  8.573  62.500   2580
  Min Nonbonded Distance : 1.836

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 16.24 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.72 (0.18), residues: 2220
  helix:  1.20 (0.17), residues: 968
  sheet:  0.18 (0.27), residues: 328
  loop : -0.06 (0.21), residues: 924

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 124 
 HIS   0.004   0.001   HIS C 233 
 PHE   0.011   0.001   PHE A 523 
 TYR   0.018   0.001   TYR D 312 
 ARG   0.011   0.001   ARG A 476 

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

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

  4440 Ramachandran restraints generated.
    2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4440 Ramachandran restraints generated.
    2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Evaluate side-chains
  344 residues out of total 1952 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 297
  time to evaluate  : 2.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   28 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8124 (mtpp)
REVERT: D  100 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7990 (mtp180)
REVERT: D  130 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8323 (mtpm)
REVERT: D  201 ASP cc_start: 0.7402 (m-30) cc_final: 0.7119 (m-30)
REVERT: D  222 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7146 (tpp-160)
REVERT: D  272 GLU cc_start: 0.7232 (mt-10) cc_final: 0.7029 (mt-10)
REVERT: A   28 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8127 (mtpp)
REVERT: A   75 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8174 (mt-10)
REVERT: A  130 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8352 (mtpm)
REVERT: A  201 ASP cc_start: 0.7451 (m-30) cc_final: 0.7153 (m-30)
REVERT: A  222 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7185 (tpp-160)
REVERT: A  272 GLU cc_start: 0.7229 (mt-10) cc_final: 0.7026 (mt-10)
REVERT: B   28 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8127 (mtpp)
REVERT: B  130 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8315 (mtpm)
REVERT: B  201 ASP cc_start: 0.7394 (m-30) cc_final: 0.7135 (m-30)
REVERT: B  219 GLU cc_start: 0.7303 (tp30) cc_final: 0.6810 (tp30)
REVERT: C   28 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8103 (mtpp)
REVERT: C  130 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8334 (mtpm)
REVERT: C  200 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7456 (ttpp)
REVERT: C  201 ASP cc_start: 0.7451 (m-30) cc_final: 0.7170 (m-30)
REVERT: C  272 GLU cc_start: 0.7212 (mt-10) cc_final: 0.7006 (mt-10)
  outliers start: 47
  outliers final: 18
  residues processed: 331
  average time/residue: 2.3485
  time to fit residues: 891.4380
Evaluate side-chains
  317 residues out of total 1952 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 287
  time to evaluate  : 2.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   12 SER
Chi-restraints excluded: chain D residue   28 LYS
Chi-restraints excluded: chain D residue  100 ARG
Chi-restraints excluded: chain D residue  130 LYS
Chi-restraints excluded: chain D residue  222 ARG
Chi-restraints excluded: chain D residue  321 SER
Chi-restraints excluded: chain D residue  539 GLU
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue   42 TYR
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue  130 LYS
Chi-restraints excluded: chain A residue  222 ARG
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain B residue   12 SER
Chi-restraints excluded: chain B residue   28 LYS
Chi-restraints excluded: chain B residue  130 LYS
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  539 GLU
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   28 LYS
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue   99 SER
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  130 LYS
Chi-restraints excluded: chain C residue  200 LYS
Chi-restraints excluded: chain C residue  321 SER
Chi-restraints excluded: chain C residue  539 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 205 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0040
   chunk 121 optimal weight:    0.9990
   chunk 155 optimal weight:    3.9990
   chunk 120 optimal weight:    1.9990
   chunk 179 optimal weight:    1.9990
   chunk 118 optimal weight:    1.9990
   chunk 212 optimal weight:    1.9990
   chunk 132 optimal weight:    0.9980
   chunk 129 optimal weight:    0.9980
   chunk 97 optimal weight:    7.9990
   overall best weight:    0.9996

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

Flipped N/Q/H residues before XYZ refinement:
D  44 ASN
D 167 GLN
D 285 GLN
D 535 GLN
A 167 GLN
A 285 GLN
A 535 GLN
B  44 ASN
B 285 GLN
C  44 ASN
C 167 GLN
C 285 GLN
C 535 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.4280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024  18136  Z= 0.245
  Angle     :  0.514   4.464  24620  Z= 0.265
  Chirality :  0.046   0.379   2784
  Planarity :  0.005   0.090   3132
  Dihedral  :  8.580  62.580   2580
  Min Nonbonded Distance : 1.809

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 16.14 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.65 (0.18), residues: 2220
  helix:  1.16 (0.17), residues: 960
  sheet:  0.17 (0.27), residues: 328
  loop : -0.12 (0.21), residues: 932

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 124 
 HIS   0.004   0.001   HIS B 233 
 PHE   0.012   0.002   PHE C 523 
 TYR   0.019   0.002   TYR D 312 
 ARG   0.011   0.001   ARG A 476 

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

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

  4440 Ramachandran restraints generated.
    2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4440 Ramachandran restraints generated.
    2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Evaluate side-chains
  347 residues out of total 1952 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 57
    poor density    : 290
  time to evaluate  : 3.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   28 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8152 (mtpp)
REVERT: D  100 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8013 (mtp180)
REVERT: D  130 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8339 (mtpm)
REVERT: D  195 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8194 (m)
REVERT: D  201 ASP cc_start: 0.7557 (m-30) cc_final: 0.7268 (m-30)
REVERT: D  222 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7146 (tpp-160)
REVERT: D  386 MET cc_start: 0.6661 (mtt) cc_final: 0.6362 (mtt)
REVERT: A   28 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8133 (mtpp)
REVERT: A   75 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8183 (mt-10)
REVERT: A  100 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7995 (mtp180)
REVERT: A  130 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8337 (mtpm)
REVERT: A  195 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8287 (t)
REVERT: A  200 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7438 (ttpp)
REVERT: A  201 ASP cc_start: 0.7529 (m-30) cc_final: 0.7245 (m-30)
REVERT: A  222 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7183 (tpp-160)
REVERT: A  272 GLU cc_start: 0.7276 (mt-10) cc_final: 0.7067 (mt-10)
REVERT: B   28 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8176 (mtpp)
REVERT: B  100 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7993 (mtp180)
REVERT: B  130 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8325 (mtpm)
REVERT: B  138 LEU cc_start: 0.8739 (mm) cc_final: 0.8426 (mt)
REVERT: B  195 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8186 (m)
REVERT: B  201 ASP cc_start: 0.7467 (m-30) cc_final: 0.7200 (m-30)
REVERT: B  272 GLU cc_start: 0.7268 (mt-10) cc_final: 0.7058 (mt-10)
REVERT: B  386 MET cc_start: 0.7029 (mtm) cc_final: 0.6760 (mtt)
REVERT: C   28 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8148 (mtpp)
REVERT: C  100 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7949 (mtp180)
REVERT: C  130 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8345 (mtpm)
REVERT: C  195 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8279 (t)
REVERT: C  200 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7472 (ttpp)
REVERT: C  201 ASP cc_start: 0.7513 (m-30) cc_final: 0.7238 (m-30)
REVERT: C  272 GLU cc_start: 0.7259 (mt-10) cc_final: 0.7050 (mt-10)
REVERT: C  386 MET cc_start: 0.6994 (mtt) cc_final: 0.6726 (mtt)
  outliers start: 57
  outliers final: 27
  residues processed: 330
  average time/residue: 2.3898
  time to fit residues: 903.8259
Evaluate side-chains
  333 residues out of total 1952 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 286
  time to evaluate  : 3.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   12 SER
Chi-restraints excluded: chain D residue   25 MET
Chi-restraints excluded: chain D residue   28 LYS
Chi-restraints excluded: chain D residue  100 ARG
Chi-restraints excluded: chain D residue  130 LYS
Chi-restraints excluded: chain D residue  195 THR
Chi-restraints excluded: chain D residue  200 LYS
Chi-restraints excluded: chain D residue  222 ARG
Chi-restraints excluded: chain D residue  321 SER
Chi-restraints excluded: chain D residue  366 LEU
Chi-restraints excluded: chain D residue  539 GLU
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue   42 TYR
Chi-restraints excluded: chain A residue   54 GLU
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue  100 ARG
Chi-restraints excluded: chain A residue  130 LYS
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  200 LYS
Chi-restraints excluded: chain A residue  222 ARG
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain B residue   12 SER
Chi-restraints excluded: chain B residue   28 LYS
Chi-restraints excluded: chain B residue   54 GLU
Chi-restraints excluded: chain B residue  100 ARG
Chi-restraints excluded: chain B residue  130 LYS
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  539 GLU
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   25 MET
Chi-restraints excluded: chain C residue   28 LYS
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue   99 SER
Chi-restraints excluded: chain C residue  100 ARG
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  130 LYS
Chi-restraints excluded: chain C residue  195 THR
Chi-restraints excluded: chain C residue  200 LYS
Chi-restraints excluded: chain C residue  321 SER
Chi-restraints excluded: chain C residue  539 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 131 optimal weight:    2.9990
   chunk 84 optimal weight:    0.8980
   chunk 126 optimal weight:    0.8980
   chunk 63 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 134 optimal weight:    0.9980
   chunk 144 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 166 optimal weight:    0.5980
   chunk 192 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
D 535 GLN
A 535 GLN
C 535 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.4350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021  18136  Z= 0.195
  Angle     :  0.488   4.364  24620  Z= 0.252
  Chirality :  0.045   0.377   2784
  Planarity :  0.005   0.087   3132
  Dihedral  :  8.449  65.290   2580
  Min Nonbonded Distance : 1.825

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.06 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.71 (0.18), residues: 2220
  helix:  1.27 (0.17), residues: 964
  sheet:  0.17 (0.28), residues: 328
  loop : -0.16 (0.21), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 124 
 HIS   0.004   0.001   HIS A 233 
 PHE   0.012   0.001   PHE B 523 
 TYR   0.015   0.001   TYR D 312 
 ARG   0.011   0.001   ARG D 476 

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

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

  4440 Ramachandran restraints generated.
    2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4440 Ramachandran restraints generated.
    2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Evaluate side-chains
  337 residues out of total 1952 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 294
  time to evaluate  : 3.044 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   28 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8172 (mtpp)
REVERT: D  100 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7995 (mtp180)
REVERT: D  130 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8337 (mtpm)
REVERT: D  138 LEU cc_start: 0.8765 (mm) cc_final: 0.8435 (mt)
REVERT: D  201 ASP cc_start: 0.7438 (m-30) cc_final: 0.7147 (m-30)
REVERT: D  222 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7158 (tpp-160)
REVERT: D  386 MET cc_start: 0.6648 (mtt) cc_final: 0.6417 (mtt)
REVERT: A   28 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8149 (mtpp)
REVERT: A   75 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8182 (mt-10)
REVERT: A  100 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7977 (mtp180)
REVERT: A  130 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8332 (mtpm)
REVERT: A  200 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7435 (ttpp)
REVERT: A  201 ASP cc_start: 0.7450 (m-30) cc_final: 0.7150 (m-30)
REVERT: A  222 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7110 (tpp-160)
REVERT: A  272 GLU cc_start: 0.7259 (mt-10) cc_final: 0.7059 (mt-10)
REVERT: B   28 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8173 (mtpp)
REVERT: B  100 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7975 (mtp180)
REVERT: B  130 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8324 (mtpm)
REVERT: B  138 LEU cc_start: 0.8727 (mm) cc_final: 0.8404 (mt)
REVERT: B  201 ASP cc_start: 0.7404 (m-30) cc_final: 0.7133 (m-30)
REVERT: B  386 MET cc_start: 0.6947 (mtm) cc_final: 0.6645 (mtt)
REVERT: C   28 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8162 (mtpp)
REVERT: C  100 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7927 (mtp180)
REVERT: C  130 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8340 (mtpm)
REVERT: C  138 LEU cc_start: 0.8765 (mm) cc_final: 0.8419 (mt)
REVERT: C  200 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7468 (ttpp)
REVERT: C  201 ASP cc_start: 0.7440 (m-30) cc_final: 0.7157 (m-30)
REVERT: C  272 GLU cc_start: 0.7247 (mt-10) cc_final: 0.7039 (mt-10)
  outliers start: 43
  outliers final: 24
  residues processed: 326
  average time/residue: 2.3522
  time to fit residues: 878.1911
Evaluate side-chains
  320 residues out of total 1952 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 280
  time to evaluate  : 2.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   12 SER
Chi-restraints excluded: chain D residue   28 LYS
Chi-restraints excluded: chain D residue  100 ARG
Chi-restraints excluded: chain D residue  130 LYS
Chi-restraints excluded: chain D residue  200 LYS
Chi-restraints excluded: chain D residue  222 ARG
Chi-restraints excluded: chain D residue  321 SER
Chi-restraints excluded: chain D residue  366 LEU
Chi-restraints excluded: chain D residue  539 GLU
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue   54 GLU
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue  100 ARG
Chi-restraints excluded: chain A residue  130 LYS
Chi-restraints excluded: chain A residue  200 LYS
Chi-restraints excluded: chain A residue  222 ARG
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain B residue   12 SER
Chi-restraints excluded: chain B residue   28 LYS
Chi-restraints excluded: chain B residue  100 ARG
Chi-restraints excluded: chain B residue  130 LYS
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  539 GLU
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   28 LYS
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue   99 SER
Chi-restraints excluded: chain C residue  100 ARG
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  130 LYS
Chi-restraints excluded: chain C residue  200 LYS
Chi-restraints excluded: chain C residue  313 THR
Chi-restraints excluded: chain C residue  321 SER
Chi-restraints excluded: chain C residue  539 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 203 optimal weight:    5.9990
   chunk 185 optimal weight:    0.4980
   chunk 197 optimal weight:    0.9980
   chunk 118 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 155 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 178 optimal weight:    0.5980
   chunk 186 optimal weight:    1.9990
   chunk 196 optimal weight:    0.4980
   chunk 129 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
D 285 GLN
D 535 GLN
A 285 GLN
A 535 GLN
B 285 GLN
B 535 GLN
C 285 GLN
C 535 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.4426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  18136  Z= 0.191
  Angle     :  0.486   4.368  24620  Z= 0.251
  Chirality :  0.045   0.378   2784
  Planarity :  0.005   0.094   3132
  Dihedral  :  8.339  67.970   2580
  Min Nonbonded Distance : 1.827

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 17.06 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.72 (0.18), residues: 2220
  helix:  1.31 (0.17), residues: 964
  sheet:  0.17 (0.28), residues: 328
  loop : -0.19 (0.21), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 124 
 HIS   0.004   0.001   HIS B 243 
 PHE   0.011   0.001   PHE C 523 
 TYR   0.020   0.001   TYR A 312 
 ARG   0.012   0.001   ARG A 476 

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

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

  4440 Ramachandran restraints generated.
    2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4440 Ramachandran restraints generated.
    2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Evaluate side-chains
  333 residues out of total 1952 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 291
  time to evaluate  : 3.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   28 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8160 (mtpp)
REVERT: D  100 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7987 (mtp180)
REVERT: D  130 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8356 (mtpm)
REVERT: D  138 LEU cc_start: 0.8760 (mm) cc_final: 0.8435 (mt)
REVERT: D  201 ASP cc_start: 0.7493 (m-30) cc_final: 0.7201 (m-30)
REVERT: D  222 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7167 (tpp-160)
REVERT: A   28 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8128 (mtpp)
REVERT: A   75 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8187 (mt-10)
REVERT: A  100 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7974 (mtp180)
REVERT: A  130 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8337 (mtpm)
REVERT: A  200 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7428 (ttpp)
REVERT: A  201 ASP cc_start: 0.7455 (m-30) cc_final: 0.7150 (m-30)
REVERT: A  222 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7115 (tpp-160)
REVERT: A  272 GLU cc_start: 0.7260 (mt-10) cc_final: 0.7060 (mt-10)
REVERT: B   28 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8156 (mtpp)
REVERT: B  100 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7974 (mtp180)
REVERT: B  130 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8329 (mtpm)
REVERT: B  201 ASP cc_start: 0.7392 (m-30) cc_final: 0.7116 (m-30)
REVERT: B  386 MET cc_start: 0.6906 (mtm) cc_final: 0.6629 (mtt)
REVERT: C   28 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8142 (mtpp)
REVERT: C  100 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8001 (mtp180)
REVERT: C  130 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8360 (mtpm)
REVERT: C  138 LEU cc_start: 0.8762 (mm) cc_final: 0.8422 (mt)
REVERT: C  200 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7461 (ttpp)
REVERT: C  201 ASP cc_start: 0.7443 (m-30) cc_final: 0.7149 (m-30)
REVERT: C  272 GLU cc_start: 0.7246 (mt-10) cc_final: 0.7038 (mt-10)
  outliers start: 42
  outliers final: 24
  residues processed: 321
  average time/residue: 2.4378
  time to fit residues: 893.7877
Evaluate side-chains
  324 residues out of total 1952 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 284
  time to evaluate  : 3.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   12 SER
Chi-restraints excluded: chain D residue   28 LYS
Chi-restraints excluded: chain D residue  100 ARG
Chi-restraints excluded: chain D residue  130 LYS
Chi-restraints excluded: chain D residue  200 LYS
Chi-restraints excluded: chain D residue  222 ARG
Chi-restraints excluded: chain D residue  313 THR
Chi-restraints excluded: chain D residue  321 SER
Chi-restraints excluded: chain D residue  366 LEU
Chi-restraints excluded: chain D residue  539 GLU
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue   54 GLU
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue  100 ARG
Chi-restraints excluded: chain A residue  130 LYS
Chi-restraints excluded: chain A residue  200 LYS
Chi-restraints excluded: chain A residue  222 ARG
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain B residue   12 SER
Chi-restraints excluded: chain B residue   28 LYS
Chi-restraints excluded: chain B residue  100 ARG
Chi-restraints excluded: chain B residue  130 LYS
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  539 GLU
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   28 LYS
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue  100 ARG
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  130 LYS
Chi-restraints excluded: chain C residue  200 LYS
Chi-restraints excluded: chain C residue  313 THR
Chi-restraints excluded: chain C residue  321 SER
Chi-restraints excluded: chain C residue  539 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 208 optimal weight:    0.5980
   chunk 127 optimal weight:    0.2980
   chunk 99 optimal weight:    3.9990
   chunk 145 optimal weight:    0.3980
   chunk 219 optimal weight:    2.9990
   chunk 201 optimal weight:    0.9980
   chunk 174 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 134 optimal weight:    0.8980
   chunk 107 optimal weight:    1.9990
   chunk 138 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
D 167 GLN
D 535 GLN
A 535 GLN
B 535 GLN
C 167 GLN
C 535 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.4479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  18136  Z= 0.176
  Angle     :  0.477   4.427  24620  Z= 0.246
  Chirality :  0.045   0.377   2784
  Planarity :  0.005   0.094   3132
  Dihedral  :  8.251  70.303   2580
  Min Nonbonded Distance : 1.838

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 17.16 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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 (0.18), residues: 2220
  helix:  1.36 (0.17), residues: 964
  sheet:  0.20 (0.28), residues: 328
  loop : -0.16 (0.21), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 392 
 HIS   0.004   0.001   HIS B 243 
 PHE   0.013   0.001   PHE D 523 
 TYR   0.017   0.001   TYR D 312 
 ARG   0.012   0.001   ARG C 476 

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

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

  4440 Ramachandran restraints generated.
    2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4440 Ramachandran restraints generated.
    2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Residue THR  433 is missing expected H atoms. Skipping.
Evaluate side-chains
  339 residues out of total 1952 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 295
  time to evaluate  : 2.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   28 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8051 (mtpp)
REVERT: D  100 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7982 (mtp180)
REVERT: D  130 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8328 (mtpm)
REVERT: D  138 LEU cc_start: 0.8754 (mm) cc_final: 0.8433 (mt)
REVERT: D  201 ASP cc_start: 0.7462 (m-30) cc_final: 0.7164 (m-30)
REVERT: D  222 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7219 (tpp-160)
REVERT: A   28 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8044 (mtpp)
REVERT: A   75 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8181 (mt-10)
REVERT: A  100 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7970 (mtp180)
REVERT: A  130 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8348 (mtpm)
REVERT: A  189 GLU cc_start: 0.7636 (tp30) cc_final: 0.7421 (tp30)
REVERT: A  200 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7425 (ttpp)
REVERT: A  201 ASP cc_start: 0.7440 (m-30) cc_final: 0.7139 (m-30)
REVERT: A  222 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7122 (tpp-160)
REVERT: B   28 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8070 (mtpp)
REVERT: B  100 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7966 (mtp180)
REVERT: B  130 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8341 (mtpm)
REVERT: B  138 LEU cc_start: 0.8729 (mm) cc_final: 0.8413 (mt)
REVERT: B  201 ASP cc_start: 0.7425 (m-30) cc_final: 0.7135 (m-30)
REVERT: C   28 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8033 (mtpp)
REVERT: C  100 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7990 (mtp180)
REVERT: C  130 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8334 (mtpm)
REVERT: C  138 LEU cc_start: 0.8768 (mm) cc_final: 0.8432 (mt)
REVERT: C  200 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7435 (ttpp)
REVERT: C  201 ASP cc_start: 0.7429 (m-30) cc_final: 0.7135 (m-30)
REVERT: C  272 GLU cc_start: 0.7229 (mt-10) cc_final: 0.7023 (mt-10)
  outliers start: 44
  outliers final: 21
  residues processed: 326
  average time/residue: 2.4324
  time to fit residues: 916.8319
Evaluate side-chains
  321 residues out of total 1952 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 284
  time to evaluate  : 2.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   12 SER
Chi-restraints excluded: chain D residue   28 LYS
Chi-restraints excluded: chain D residue  100 ARG
Chi-restraints excluded: chain D residue  130 LYS
Chi-restraints excluded: chain D residue  222 ARG
Chi-restraints excluded: chain D residue  313 THR
Chi-restraints excluded: chain D residue  321 SER
Chi-restraints excluded: chain D residue  366 LEU
Chi-restraints excluded: chain D residue  539 GLU
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue  100 ARG
Chi-restraints excluded: chain A residue  130 LYS
Chi-restraints excluded: chain A residue  200 LYS
Chi-restraints excluded: chain A residue  222 ARG
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain B residue   12 SER
Chi-restraints excluded: chain B residue   28 LYS
Chi-restraints excluded: chain B residue  100 ARG
Chi-restraints excluded: chain B residue  130 LYS
Chi-restraints excluded: chain B residue  200 LYS
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   28 LYS
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue  100 ARG
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  130 LYS
Chi-restraints excluded: chain C residue  200 LYS
Chi-restraints excluded: chain C residue  313 THR
Chi-restraints excluded: chain C residue  321 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 185 optimal weight:    0.7980
   chunk 53 optimal weight:    0.5980
   chunk 160 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 174 optimal weight:    0.9990
   chunk 73 optimal weight:    0.6980
   chunk 179 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 153 optimal weight:    8.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
D 285 GLN
D 336 GLN
D 535 GLN
A 285 GLN
A 336 GLN
A 535 GLN
B 167 GLN
B 285 GLN
B 535 GLN
C 285 GLN
C 535 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.176117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.126755 restraints weight = 55469.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 1.92
r_work: 0.3167 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.4519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  18136  Z= 0.205
  Angle     :  0.492   4.332  24620  Z= 0.254
  Chirality :  0.046   0.377   2784
  Planarity :  0.005   0.084   3132
  Dihedral  :  8.263  71.691   2580
  Min Nonbonded Distance : 1.826

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.57 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.71 (0.18), residues: 2220
  helix:  1.29 (0.17), residues: 968
  sheet:  0.24 (0.28), residues: 328
  loop : -0.21 (0.21), residues: 924

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 392 
 HIS   0.004   0.001   HIS B 243 
 PHE   0.012   0.002   PHE C 523 
 TYR   0.019   0.001   TYR D 312 
 ARG   0.011   0.001   ARG A 476 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 14470.06 seconds
wall clock time: 253 minutes 4.09 seconds (15184.09 seconds total)