Starting phenix.real_space_refine
on Mon Mar 18 02:44:51 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbf_21588/03_2024/6wbf_21588_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbf_21588/03_2024/6wbf_21588.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbf_21588/03_2024/6wbf_21588.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbf_21588/03_2024/6wbf_21588.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbf_21588/03_2024/6wbf_21588_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbf_21588/03_2024/6wbf_21588_updated.pdb"
  }
  resolution = 2.83
  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=   0.001 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      21      5.49       5
     S      77      5.16       5
     C   13321      2.51       5
     N    2912      2.21       5
     O    3381      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG  217": "NH1" <-> "NH2"
    Residue "A ARG  254": "NH1" <-> "NH2"
    Residue "A GLU  336": "OE1" <-> "OE2"
    Residue "B ARG  217": "NH1" <-> "NH2"
    Residue "B ARG  254": "NH1" <-> "NH2"
    Residue "B GLU  336": "OE1" <-> "OE2"
    Residue "C ARG  217": "NH1" <-> "NH2"
    Residue "C ARG  254": "NH1" <-> "NH2"
    Residue "C GLU  336": "OE1" <-> "OE2"
    Residue "D ARG  217": "NH1" <-> "NH2"
    Residue "D ARG  254": "NH1" <-> "NH2"
    Residue "D GLU  336": "OE1" <-> "OE2"
    Residue "E ARG  217": "NH1" <-> "NH2"
    Residue "E ARG  254": "NH1" <-> "NH2"
    Residue "E GLU  336": "OE1" <-> "OE2"
    Residue "F ARG  217": "NH1" <-> "NH2"
    Residue "F ARG  254": "NH1" <-> "NH2"
    Residue "F GLU  336": "OE1" <-> "OE2"
    Residue "G ARG  217": "NH1" <-> "NH2"
    Residue "G ARG  254": "NH1" <-> "NH2"
    Residue "G GLU  336": "OE1" <-> "OE2"
  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: 19712
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 2598
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2598
          Classifications: {'peptide': 344}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 15, 'TRANS': 328}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 164
          Unresolved non-hydrogen angles: 202
          Unresolved non-hydrogen dihedrals: 134
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 89
    Chain: "B"
      Number of atoms: 2598
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2598
          Classifications: {'peptide': 344}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 15, 'TRANS': 328}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 164
          Unresolved non-hydrogen angles: 202
          Unresolved non-hydrogen dihedrals: 134
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 89
    Chain: "C"
      Number of atoms: 2598
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2598
          Classifications: {'peptide': 344}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 15, 'TRANS': 328}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 164
          Unresolved non-hydrogen angles: 202
          Unresolved non-hydrogen dihedrals: 134
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 89
    Chain: "D"
      Number of atoms: 2598
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2598
          Classifications: {'peptide': 344}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 15, 'TRANS': 328}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 164
          Unresolved non-hydrogen angles: 202
          Unresolved non-hydrogen dihedrals: 134
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 89
    Chain: "E"
      Number of atoms: 2598
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2598
          Classifications: {'peptide': 344}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 15, 'TRANS': 328}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 164
          Unresolved non-hydrogen angles: 202
          Unresolved non-hydrogen dihedrals: 134
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 89
    Chain: "F"
      Number of atoms: 2598
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2598
          Classifications: {'peptide': 344}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 15, 'TRANS': 328}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 164
          Unresolved non-hydrogen angles: 202
          Unresolved non-hydrogen dihedrals: 134
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 89
    Chain: "G"
      Number of atoms: 2598
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2598
          Classifications: {'peptide': 344}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 15, 'TRANS': 328}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 164
          Unresolved non-hydrogen angles: 202
          Unresolved non-hydrogen dihedrals: 134
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 89
    Chain: "A"
      Number of atoms: 218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 218
          Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 218
          Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 218
          Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 218
          Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 218
          Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 218
          Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 1
    Chain: "G"
      Number of atoms: 218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 218
          Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 10.61, per 1000 atoms: 0.54
  Number of scatterers: 19712
  At special positions: 0
  Unit cell: (107.73, 108.756, 121.068, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      77     16.00
     P      21     15.00
     O    3381      8.00
     N    2912      7.00
     C   13321      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  66 " - pdb=" SG  CYS A 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  84 " - pdb=" SG  CYS A 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  66 " - pdb=" SG  CYS B 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  84 " - pdb=" SG  CYS B 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  66 " - pdb=" SG  CYS C 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  84 " - pdb=" SG  CYS C 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  66 " - pdb=" SG  CYS D 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  84 " - pdb=" SG  CYS D 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  66 " - pdb=" SG  CYS E 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  84 " - pdb=" SG  CYS E 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  66 " - pdb=" SG  CYS F 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  84 " - pdb=" SG  CYS F 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  66 " - pdb=" SG  CYS G 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  84 " - pdb=" SG  CYS G 246 " distance=2.03

  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
  Links applied
    NAG-ASN
      " NAG A 407 " - " ASN A 255 "
      " NAG B 407 " - " ASN B 255 "
      " NAG C 407 " - " ASN C 255 "
      " NAG D 407 " - " ASN D 255 "
      " NAG E 407 " - " ASN E 255 "
      " NAG F 407 " - " ASN F 255 "
      " NAG G 407 " - " ASN G 255 "
  Time building additional restraints: 7.43
  Conformation dependent library (CDL) restraints added in 3.1 seconds
  

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4662

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      105 helices and 7 sheets defined
      63.7% alpha, 1.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 10
    Processing helix  chain 'A' and resid 33 through 53
      Proline residue:  A  46  - end of helix
    Processing helix  chain 'A' and resid 74 through 88
    Processing helix  chain 'A' and resid 100 through 107
    Processing helix  chain 'A' and resid 109 through 130
      Proline residue:  A 123  - end of helix
    Processing helix  chain 'A' and resid 132 through 161
    Processing helix  chain 'A' and resid 195 through 203
    Processing helix  chain 'A' and resid 208 through 235
    Processing helix  chain 'A' and resid 251 through 253
      No H-bonds generated for 'chain 'A' and resid 251 through 253'
    Processing helix  chain 'A' and resid 270 through 295
      Proline residue:  A 289  - end of helix
    Processing helix  chain 'A' and resid 297 through 300
      No H-bonds generated for 'chain 'A' and resid 297 through 300'
    Processing helix  chain 'A' and resid 305 through 311
      removed outlier: 4.013A  pdb=" N   ILE A 311 " --> pdb=" O   VAL A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 341
      removed outlier: 5.148A  pdb=" N   SER A 340 " --> pdb=" O   GLU A 336 " (cutoff:3.500A)
      removed outlier: 5.601A  pdb=" N   GLU A 341 " --> pdb=" O   GLU A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 357
      removed outlier: 4.276A  pdb=" N   SER A 357 " --> pdb=" O   ASN A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 369
    Processing helix  chain 'B' and resid 3 through 10
    Processing helix  chain 'B' and resid 33 through 53
      Proline residue:  B  46  - end of helix
    Processing helix  chain 'B' and resid 74 through 88
    Processing helix  chain 'B' and resid 100 through 107
    Processing helix  chain 'B' and resid 109 through 130
      Proline residue:  B 123  - end of helix
    Processing helix  chain 'B' and resid 132 through 161
    Processing helix  chain 'B' and resid 195 through 203
    Processing helix  chain 'B' and resid 208 through 235
    Processing helix  chain 'B' and resid 251 through 253
      No H-bonds generated for 'chain 'B' and resid 251 through 253'
    Processing helix  chain 'B' and resid 270 through 295
      Proline residue:  B 289  - end of helix
    Processing helix  chain 'B' and resid 297 through 300
      No H-bonds generated for 'chain 'B' and resid 297 through 300'
    Processing helix  chain 'B' and resid 305 through 311
      removed outlier: 4.014A  pdb=" N   ILE B 311 " --> pdb=" O   VAL B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 341
      removed outlier: 5.148A  pdb=" N   SER B 340 " --> pdb=" O   GLU B 336 " (cutoff:3.500A)
      removed outlier: 5.601A  pdb=" N   GLU B 341 " --> pdb=" O   GLU B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 343 through 357
      removed outlier: 4.277A  pdb=" N   SER B 357 " --> pdb=" O   ASN B 353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 362 through 369
    Processing helix  chain 'C' and resid 3 through 10
    Processing helix  chain 'C' and resid 33 through 53
      Proline residue:  C  46  - end of helix
    Processing helix  chain 'C' and resid 74 through 88
    Processing helix  chain 'C' and resid 100 through 107
    Processing helix  chain 'C' and resid 109 through 130
      Proline residue:  C 123  - end of helix
    Processing helix  chain 'C' and resid 132 through 161
    Processing helix  chain 'C' and resid 195 through 203
    Processing helix  chain 'C' and resid 208 through 235
    Processing helix  chain 'C' and resid 251 through 253
      No H-bonds generated for 'chain 'C' and resid 251 through 253'
    Processing helix  chain 'C' and resid 270 through 295
      Proline residue:  C 289  - end of helix
    Processing helix  chain 'C' and resid 297 through 300
      No H-bonds generated for 'chain 'C' and resid 297 through 300'
    Processing helix  chain 'C' and resid 305 through 311
      removed outlier: 4.013A  pdb=" N   ILE C 311 " --> pdb=" O   VAL C 308 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 327 through 341
      removed outlier: 5.149A  pdb=" N   SER C 340 " --> pdb=" O   GLU C 336 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   GLU C 341 " --> pdb=" O   GLU C 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 343 through 357
      removed outlier: 4.277A  pdb=" N   SER C 357 " --> pdb=" O   ASN C 353 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 362 through 369
    Processing helix  chain 'D' and resid 3 through 10
    Processing helix  chain 'D' and resid 33 through 53
      Proline residue:  D  46  - end of helix
    Processing helix  chain 'D' and resid 74 through 88
    Processing helix  chain 'D' and resid 100 through 107
    Processing helix  chain 'D' and resid 109 through 130
      Proline residue:  D 123  - end of helix
    Processing helix  chain 'D' and resid 132 through 161
    Processing helix  chain 'D' and resid 195 through 203
    Processing helix  chain 'D' and resid 208 through 235
    Processing helix  chain 'D' and resid 251 through 253
      No H-bonds generated for 'chain 'D' and resid 251 through 253'
    Processing helix  chain 'D' and resid 270 through 295
      Proline residue:  D 289  - end of helix
    Processing helix  chain 'D' and resid 297 through 300
      No H-bonds generated for 'chain 'D' and resid 297 through 300'
    Processing helix  chain 'D' and resid 305 through 311
      removed outlier: 4.013A  pdb=" N   ILE D 311 " --> pdb=" O   VAL D 308 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 327 through 341
      removed outlier: 5.149A  pdb=" N   SER D 340 " --> pdb=" O   GLU D 336 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   GLU D 341 " --> pdb=" O   GLU D 337 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 343 through 357
      removed outlier: 4.276A  pdb=" N   SER D 357 " --> pdb=" O   ASN D 353 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 362 through 369
    Processing helix  chain 'E' and resid 3 through 10
    Processing helix  chain 'E' and resid 33 through 53
      Proline residue:  E  46  - end of helix
    Processing helix  chain 'E' and resid 74 through 88
    Processing helix  chain 'E' and resid 100 through 107
    Processing helix  chain 'E' and resid 109 through 130
      Proline residue:  E 123  - end of helix
    Processing helix  chain 'E' and resid 132 through 161
    Processing helix  chain 'E' and resid 195 through 203
    Processing helix  chain 'E' and resid 208 through 235
    Processing helix  chain 'E' and resid 251 through 253
      No H-bonds generated for 'chain 'E' and resid 251 through 253'
    Processing helix  chain 'E' and resid 270 through 295
      Proline residue:  E 289  - end of helix
    Processing helix  chain 'E' and resid 297 through 300
      No H-bonds generated for 'chain 'E' and resid 297 through 300'
    Processing helix  chain 'E' and resid 305 through 311
      removed outlier: 4.012A  pdb=" N   ILE E 311 " --> pdb=" O   VAL E 308 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 327 through 341
      removed outlier: 5.147A  pdb=" N   SER E 340 " --> pdb=" O   GLU E 336 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   GLU E 341 " --> pdb=" O   GLU E 337 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 343 through 357
      removed outlier: 4.276A  pdb=" N   SER E 357 " --> pdb=" O   ASN E 353 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 362 through 369
    Processing helix  chain 'F' and resid 3 through 10
    Processing helix  chain 'F' and resid 33 through 53
      Proline residue:  F  46  - end of helix
    Processing helix  chain 'F' and resid 74 through 88
    Processing helix  chain 'F' and resid 100 through 107
    Processing helix  chain 'F' and resid 109 through 130
      Proline residue:  F 123  - end of helix
    Processing helix  chain 'F' and resid 132 through 161
    Processing helix  chain 'F' and resid 195 through 203
    Processing helix  chain 'F' and resid 208 through 235
    Processing helix  chain 'F' and resid 251 through 253
      No H-bonds generated for 'chain 'F' and resid 251 through 253'
    Processing helix  chain 'F' and resid 270 through 295
      Proline residue:  F 289  - end of helix
    Processing helix  chain 'F' and resid 297 through 300
      No H-bonds generated for 'chain 'F' and resid 297 through 300'
    Processing helix  chain 'F' and resid 305 through 311
      removed outlier: 4.013A  pdb=" N   ILE F 311 " --> pdb=" O   VAL F 308 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 327 through 341
      removed outlier: 5.148A  pdb=" N   SER F 340 " --> pdb=" O   GLU F 336 " (cutoff:3.500A)
      removed outlier: 5.601A  pdb=" N   GLU F 341 " --> pdb=" O   GLU F 337 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 343 through 357
      removed outlier: 4.276A  pdb=" N   SER F 357 " --> pdb=" O   ASN F 353 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 362 through 369
    Processing helix  chain 'G' and resid 3 through 10
    Processing helix  chain 'G' and resid 33 through 53
      Proline residue:  G  46  - end of helix
    Processing helix  chain 'G' and resid 74 through 88
    Processing helix  chain 'G' and resid 100 through 107
    Processing helix  chain 'G' and resid 109 through 130
      Proline residue:  G 123  - end of helix
    Processing helix  chain 'G' and resid 132 through 161
    Processing helix  chain 'G' and resid 195 through 203
    Processing helix  chain 'G' and resid 208 through 235
    Processing helix  chain 'G' and resid 251 through 253
      No H-bonds generated for 'chain 'G' and resid 251 through 253'
    Processing helix  chain 'G' and resid 270 through 295
      Proline residue:  G 289  - end of helix
    Processing helix  chain 'G' and resid 297 through 300
      No H-bonds generated for 'chain 'G' and resid 297 through 300'
    Processing helix  chain 'G' and resid 305 through 311
      removed outlier: 4.012A  pdb=" N   ILE G 311 " --> pdb=" O   VAL G 308 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 327 through 341
      removed outlier: 5.148A  pdb=" N   SER G 340 " --> pdb=" O   GLU G 336 " (cutoff:3.500A)
      removed outlier: 5.603A  pdb=" N   GLU G 341 " --> pdb=" O   GLU G 337 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 343 through 357
      removed outlier: 4.275A  pdb=" N   SER G 357 " --> pdb=" O   ASN G 353 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 362 through 369
    Processing sheet with id=  A, first strand: chain 'A' and resid 243 through 246
    Processing sheet with id=  B, first strand: chain 'B' and resid 243 through 246
    Processing sheet with id=  C, first strand: chain 'C' and resid 243 through 246
    Processing sheet with id=  D, first strand: chain 'D' and resid 243 through 246
    Processing sheet with id=  E, first strand: chain 'E' and resid 243 through 246
    Processing sheet with id=  F, first strand: chain 'F' and resid 243 through 246
    Processing sheet with id=  G, first strand: chain 'G' and resid 243 through 246

    1064 hydrogen bonds defined for protein.
    3108 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.69

  Time building geometry restraints manager: 8.10 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2895
        1.32 -     1.44: 5035
        1.44 -     1.57: 12083
        1.57 -     1.69: 42
        1.69 -     1.81: 91
  Bond restraints: 20146
  Sorted by residual:
  bond pdb=" N   ASN A 369 "
       pdb=" CA  ASN A 369 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.17e-02 7.31e+03 9.38e+00
  bond pdb=" N   ASN F 369 "
       pdb=" CA  ASN F 369 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.034 1.17e-02 7.31e+03 8.66e+00
  bond pdb=" N   ASN C 369 "
       pdb=" CA  ASN C 369 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.034 1.17e-02 7.31e+03 8.62e+00
  bond pdb=" N   ASN D 369 "
       pdb=" CA  ASN D 369 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.035 1.29e-02 6.01e+03 7.44e+00
  bond pdb=" N   ASN G 369 "
       pdb=" CA  ASN G 369 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.034 1.29e-02 6.01e+03 7.11e+00
  ... (remaining 20141 not shown)

  Histogram of bond angle deviations from ideal:
       98.70 -   105.77: 462
      105.77 -   112.83: 11162
      112.83 -   119.90: 6767
      119.90 -   126.96: 8750
      126.96 -   134.03: 187
  Bond angle restraints: 27328
  Sorted by residual:
  angle pdb=" C   TYR E  10 "
        pdb=" N   VAL E  11 "
        pdb=" CA  VAL E  11 "
      ideal   model   delta    sigma   weight residual
     122.77  118.80    3.97 1.05e+00 9.07e-01 1.43e+01
  angle pdb=" C   TYR B  10 "
        pdb=" N   VAL B  11 "
        pdb=" CA  VAL B  11 "
      ideal   model   delta    sigma   weight residual
     122.77  118.88    3.89 1.05e+00 9.07e-01 1.37e+01
  angle pdb=" C   TYR D  10 "
        pdb=" N   VAL D  11 "
        pdb=" CA  VAL D  11 "
      ideal   model   delta    sigma   weight residual
     122.77  118.91    3.86 1.05e+00 9.07e-01 1.35e+01
  angle pdb=" C   TYR F  10 "
        pdb=" N   VAL F  11 "
        pdb=" CA  VAL F  11 "
      ideal   model   delta    sigma   weight residual
     122.77  118.91    3.86 1.05e+00 9.07e-01 1.35e+01
  angle pdb=" C   TYR A  10 "
        pdb=" N   VAL A  11 "
        pdb=" CA  VAL A  11 "
      ideal   model   delta    sigma   weight residual
     122.77  118.92    3.85 1.05e+00 9.07e-01 1.34e+01
  ... (remaining 27323 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.69: 12379
       29.69 -    59.39: 622
       59.39 -    89.08: 32
       89.08 -   118.77: 1
      118.77 -   148.47: 14
  Dihedral angle restraints: 13048
    sinusoidal: 5873
      harmonic: 7175
  Sorted by residual:
  dihedral pdb=" N1  PTY A 401 "
           pdb=" C2  PTY A 401 "
           pdb=" C3  PTY A 401 "
           pdb=" O11 PTY A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      65.33  -83.14  148.47     1      3.00e+01 1.11e-03 1.98e+01
  dihedral pdb=" N1  PTY D 401 "
           pdb=" C2  PTY D 401 "
           pdb=" C3  PTY D 401 "
           pdb=" O11 PTY D 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      65.33  -83.11  148.44     1      3.00e+01 1.11e-03 1.98e+01
  dihedral pdb=" N1  PTY B 401 "
           pdb=" C2  PTY B 401 "
           pdb=" C3  PTY B 401 "
           pdb=" O11 PTY B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      65.33  -83.09  148.42     1      3.00e+01 1.11e-03 1.98e+01
  ... (remaining 13045 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 2253
       0.038 -    0.076: 719
       0.076 -    0.114: 228
       0.114 -    0.152: 41
       0.152 -    0.191: 14
  Chirality restraints: 3255
  Sorted by residual:
  chirality pdb=" CA  ILE E 373 "
            pdb=" N   ILE E 373 "
            pdb=" C   ILE E 373 "
            pdb=" CB  ILE E 373 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 9.07e-01
  chirality pdb=" CA  ILE D 373 "
            pdb=" N   ILE D 373 "
            pdb=" C   ILE D 373 "
            pdb=" CB  ILE D 373 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.78e-01
  chirality pdb=" CA  ILE A 373 "
            pdb=" N   ILE A 373 "
            pdb=" C   ILE A 373 "
            pdb=" CB  ILE A 373 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.68e-01
  ... (remaining 3252 not shown)

  Planarity restraints: 3185
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG G 407 "   -0.090 2.00e-02 2.50e+03   7.40e-02 6.84e+01
        pdb=" C7  NAG G 407 "    0.026 2.00e-02 2.50e+03
        pdb=" C8  NAG G 407 "   -0.069 2.00e-02 2.50e+03
        pdb=" N2  NAG G 407 "    0.116 2.00e-02 2.50e+03
        pdb=" O7  NAG G 407 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F 407 "    0.090 2.00e-02 2.50e+03   7.39e-02 6.84e+01
        pdb=" C7  NAG F 407 "   -0.026 2.00e-02 2.50e+03
        pdb=" C8  NAG F 407 "    0.069 2.00e-02 2.50e+03
        pdb=" N2  NAG F 407 "   -0.117 2.00e-02 2.50e+03
        pdb=" O7  NAG F 407 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 407 "   -0.090 2.00e-02 2.50e+03   7.39e-02 6.82e+01
        pdb=" C7  NAG B 407 "    0.027 2.00e-02 2.50e+03
        pdb=" C8  NAG B 407 "   -0.069 2.00e-02 2.50e+03
        pdb=" N2  NAG B 407 "    0.116 2.00e-02 2.50e+03
        pdb=" O7  NAG B 407 "    0.016 2.00e-02 2.50e+03
  ... (remaining 3182 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 1404
        2.73 -     3.27: 20995
        3.27 -     3.81: 33355
        3.81 -     4.36: 39895
        4.36 -     4.90: 68982
  Nonbonded interactions: 164631
  Sorted by model distance:
  nonbonded pdb=" O   LEU A  52 "
            pdb=" OH  TYR G 111 "
     model   vdw
     2.183 2.440
  nonbonded pdb=" OH  TYR C 111 "
            pdb=" O   LEU D  52 "
     model   vdw
     2.184 2.440
  nonbonded pdb=" OH  TYR B 111 "
            pdb=" O   LEU C  52 "
     model   vdw
     2.186 2.440
  nonbonded pdb=" OH  TYR F 111 "
            pdb=" O   LEU G  52 "
     model   vdw
     2.190 2.440
  nonbonded pdb=" OH  TYR E 111 "
            pdb=" O   LEU F  52 "
     model   vdw
     2.193 2.440
  ... (remaining 164626 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

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:             0.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          3.910
  Check model and map are aligned:         0.310
  Set scattering table:                    0.200
  Process input model:                     50.400
  Find NCS groups from input model:        1.350
  Set up NCS constraints:                  0.140
  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:11.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   68.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5870
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      :  0.007   0.049  20146  Z= 0.440
  Angle     :  0.826  10.089  27328  Z= 0.455
  Chirality :  0.043   0.191   3255
  Planarity :  0.005   0.074   3178
  Dihedral  : 16.595 148.466   8344
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  6.14 %
    Favored  : 93.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.16), residues: 2380
  helix: -0.08 (0.12), residues: 1603
  sheet:  None (None), residues: 0
  loop : -2.81 (0.20), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 104 
 HIS   0.002   0.001   HIS A 106 
 PHE   0.013   0.002   PHE B  54 
 TYR   0.015   0.001   TYR E  10 
 ARG   0.002   0.000   ARG E 152 

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

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

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  524 residues out of total 2177 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 517
  time to evaluate  : 2.056 
Fit side-chains
REVERT: A    9 GLU cc_start: 0.6351 (tt0) cc_final: 0.5963 (mm-30)
REVERT: A   35 ASP cc_start: 0.6726 (m-30) cc_final: 0.6444 (m-30)
REVERT: A   56 GLN cc_start: 0.6870 (tp-100) cc_final: 0.6250 (tt0)
REVERT: A   65 SER cc_start: 0.8400 (m) cc_final: 0.7727 (p)
REVERT: A   74 TRP cc_start: 0.7067 (t60) cc_final: 0.6512 (t-100)
REVERT: A  100 ASN cc_start: 0.7285 (m-40) cc_final: 0.7046 (m110)
REVERT: A  111 TYR cc_start: 0.7491 (m-10) cc_final: 0.6300 (m-10)
REVERT: A  135 ILE cc_start: 0.6230 (tt) cc_final: 0.6008 (mt)
REVERT: A  201 LYS cc_start: 0.6877 (tppp) cc_final: 0.6640 (tppt)
REVERT: A  208 ASN cc_start: 0.5723 (t0) cc_final: 0.5456 (t0)
REVERT: A  212 LYS cc_start: 0.5550 (mttt) cc_final: 0.5226 (mttp)
REVERT: A  254 ARG cc_start: 0.6826 (ttm110) cc_final: 0.6586 (ttm-80)
REVERT: A  338 ASN cc_start: 0.6514 (m-40) cc_final: 0.6288 (m-40)
REVERT: A  348 LEU cc_start: 0.6310 (mt) cc_final: 0.6001 (mt)
REVERT: B   35 ASP cc_start: 0.6571 (m-30) cc_final: 0.6205 (m-30)
REVERT: B   56 GLN cc_start: 0.6777 (tp-100) cc_final: 0.6083 (tt0)
REVERT: B   74 TRP cc_start: 0.7493 (t60) cc_final: 0.7062 (t-100)
REVERT: B  100 ASN cc_start: 0.7434 (m-40) cc_final: 0.6471 (t0)
REVERT: B  111 TYR cc_start: 0.7354 (m-10) cc_final: 0.6153 (m-10)
REVERT: B  129 PHE cc_start: 0.8078 (m-80) cc_final: 0.7876 (m-80)
REVERT: B  135 ILE cc_start: 0.6221 (tt) cc_final: 0.5865 (mt)
REVERT: B  201 LYS cc_start: 0.6843 (tppp) cc_final: 0.6581 (tppt)
REVERT: B  217 ARG cc_start: 0.6654 (mmp-170) cc_final: 0.6387 (mmp80)
REVERT: B  219 LEU cc_start: 0.6726 (mp) cc_final: 0.6474 (mp)
REVERT: B  229 ILE cc_start: 0.7415 (mt) cc_final: 0.7153 (mm)
REVERT: B  242 ASP cc_start: 0.7737 (p0) cc_final: 0.7521 (p0)
REVERT: B  254 ARG cc_start: 0.6805 (ttm110) cc_final: 0.6509 (ttt180)
REVERT: B  262 GLN cc_start: 0.8084 (pt0) cc_final: 0.7859 (pt0)
REVERT: B  348 LEU cc_start: 0.6460 (mt) cc_final: 0.6252 (mt)
REVERT: C   35 ASP cc_start: 0.6476 (m-30) cc_final: 0.6220 (m-30)
REVERT: C   74 TRP cc_start: 0.7291 (t60) cc_final: 0.6554 (t-100)
REVERT: C  100 ASN cc_start: 0.7341 (m-40) cc_final: 0.6279 (t0)
REVERT: C  111 TYR cc_start: 0.7236 (m-10) cc_final: 0.5993 (m-10)
REVERT: C  139 LEU cc_start: 0.5468 (tp) cc_final: 0.5228 (tp)
REVERT: C  201 LYS cc_start: 0.6764 (tppp) cc_final: 0.6360 (tmmt)
REVERT: C  208 ASN cc_start: 0.5808 (t0) cc_final: 0.5596 (t0)
REVERT: C  222 ILE cc_start: 0.7129 (mm) cc_final: 0.6892 (mt)
REVERT: C  229 ILE cc_start: 0.7416 (mt) cc_final: 0.7133 (mm)
REVERT: C  254 ARG cc_start: 0.6905 (ttm110) cc_final: 0.6658 (ttm-80)
REVERT: C  299 PHE cc_start: 0.6183 (t80) cc_final: 0.5715 (t80)
REVERT: C  345 TYR cc_start: 0.7119 (t80) cc_final: 0.6813 (t80)
REVERT: D    9 GLU cc_start: 0.6323 (tt0) cc_final: 0.5933 (mm-30)
REVERT: D   35 ASP cc_start: 0.6595 (m-30) cc_final: 0.6231 (m-30)
REVERT: D   36 LYS cc_start: 0.6543 (ttmm) cc_final: 0.6309 (ttmt)
REVERT: D   50 ILE cc_start: 0.7160 (mt) cc_final: 0.6943 (mm)
REVERT: D   56 GLN cc_start: 0.6961 (tp-100) cc_final: 0.6289 (tt0)
REVERT: D   74 TRP cc_start: 0.7263 (t60) cc_final: 0.6857 (t-100)
REVERT: D  100 ASN cc_start: 0.7333 (m-40) cc_final: 0.6412 (t0)
REVERT: D  111 TYR cc_start: 0.7226 (m-10) cc_final: 0.6016 (m-10)
REVERT: D  201 LYS cc_start: 0.6509 (tppp) cc_final: 0.6287 (tppt)
REVERT: D  208 ASN cc_start: 0.5939 (t0) cc_final: 0.5680 (t0)
REVERT: D  212 LYS cc_start: 0.5851 (mttt) cc_final: 0.5580 (mttp)
REVERT: D  229 ILE cc_start: 0.7671 (mt) cc_final: 0.7449 (mm)
REVERT: D  254 ARG cc_start: 0.6806 (ttm110) cc_final: 0.6423 (ttm-80)
REVERT: D  262 GLN cc_start: 0.8155 (pt0) cc_final: 0.7931 (pt0)
REVERT: D  296 PHE cc_start: 0.7139 (m-80) cc_final: 0.6788 (m-80)
REVERT: D  338 ASN cc_start: 0.6740 (m-40) cc_final: 0.6535 (m-40)
REVERT: E   36 LYS cc_start: 0.6210 (ttmm) cc_final: 0.5612 (ttpt)
REVERT: E   65 SER cc_start: 0.8369 (m) cc_final: 0.7706 (p)
REVERT: E   74 TRP cc_start: 0.7355 (t60) cc_final: 0.6996 (t-100)
REVERT: E  100 ASN cc_start: 0.7525 (m-40) cc_final: 0.6344 (t0)
REVERT: E  111 TYR cc_start: 0.7330 (m-10) cc_final: 0.6215 (m-10)
REVERT: E  129 PHE cc_start: 0.8093 (m-80) cc_final: 0.7664 (m-80)
REVERT: E  135 ILE cc_start: 0.6353 (tt) cc_final: 0.6078 (mt)
REVERT: E  139 LEU cc_start: 0.5757 (tp) cc_final: 0.5347 (tp)
REVERT: E  201 LYS cc_start: 0.6866 (tppp) cc_final: 0.6496 (tmmt)
REVERT: E  222 ILE cc_start: 0.7367 (mm) cc_final: 0.7009 (mt)
REVERT: E  229 ILE cc_start: 0.7596 (mt) cc_final: 0.7343 (mm)
REVERT: E  254 ARG cc_start: 0.6777 (ttm110) cc_final: 0.6447 (ttm-80)
REVERT: E  262 GLN cc_start: 0.8199 (pt0) cc_final: 0.7983 (pt0)
REVERT: E  296 PHE cc_start: 0.7097 (m-80) cc_final: 0.6812 (m-80)
REVERT: F   31 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6795 (tt0)
REVERT: F   35 ASP cc_start: 0.6668 (m-30) cc_final: 0.6464 (m-30)
REVERT: F  100 ASN cc_start: 0.7339 (m-40) cc_final: 0.6533 (t0)
REVERT: F  111 TYR cc_start: 0.7294 (m-10) cc_final: 0.5963 (m-10)
REVERT: F  139 LEU cc_start: 0.5547 (tp) cc_final: 0.5287 (tp)
REVERT: F  201 LYS cc_start: 0.6588 (tppp) cc_final: 0.6231 (tmmt)
REVERT: F  212 LYS cc_start: 0.5669 (mttt) cc_final: 0.5452 (mttp)
REVERT: F  229 ILE cc_start: 0.7753 (mt) cc_final: 0.7494 (mm)
REVERT: F  254 ARG cc_start: 0.6744 (ttm110) cc_final: 0.6433 (ttt180)
REVERT: F  262 GLN cc_start: 0.8118 (pt0) cc_final: 0.7908 (pt0)
REVERT: G    5 GLN cc_start: 0.6074 (mt0) cc_final: 0.5854 (tp40)
REVERT: G    9 GLU cc_start: 0.6184 (tt0) cc_final: 0.5947 (mp0)
REVERT: G   50 ILE cc_start: 0.7297 (mt) cc_final: 0.7089 (mm)
REVERT: G   75 ARG cc_start: 0.7628 (mmt180) cc_final: 0.7225 (mmt180)
REVERT: G  100 ASN cc_start: 0.7452 (m-40) cc_final: 0.6474 (t0)
REVERT: G  111 TYR cc_start: 0.7407 (m-10) cc_final: 0.6251 (m-10)
REVERT: G  201 LYS cc_start: 0.6611 (tppp) cc_final: 0.6342 (tppt)
REVERT: G  217 ARG cc_start: 0.6817 (mmp-170) cc_final: 0.6549 (mmp80)
REVERT: G  219 LEU cc_start: 0.6619 (mp) cc_final: 0.6377 (mt)
REVERT: G  222 ILE cc_start: 0.6956 (mm) cc_final: 0.6571 (mp)
REVERT: G  229 ILE cc_start: 0.7855 (mt) cc_final: 0.7597 (mp)
REVERT: G  254 ARG cc_start: 0.7049 (ttm110) cc_final: 0.6641 (ttm-80)
REVERT: G  296 PHE cc_start: 0.7006 (m-80) cc_final: 0.6068 (m-80)
REVERT: G  338 ASN cc_start: 0.6838 (m-40) cc_final: 0.6504 (m-40)
  outliers start: 7
  outliers final: 0
  residues processed: 521
  average time/residue: 1.1514
  time to fit residues: 683.1827
Evaluate side-chains
  375 residues out of total 2177 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 375
  time to evaluate  : 1.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 238
   random chunks:
   chunk 200 optimal weight:    4.9990
   chunk 180 optimal weight:    0.4980
   chunk 100 optimal weight:   10.0000
   chunk 61 optimal weight:    5.9990
   chunk 121 optimal weight:    0.6980
   chunk 96 optimal weight:    3.9990
   chunk 186 optimal weight:   10.0000
   chunk 72 optimal weight:    0.9980
   chunk 113 optimal weight:    0.6980
   chunk 138 optimal weight:    0.0170
   chunk 216 optimal weight:    0.6980
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
A  89 GLN
A  90 GLN
A  92 ASN
A 134 HIS
A 332 ASN
A 353 ASN
B  76 GLN
B  89 GLN
C  76 GLN
C  89 GLN
C  90 GLN
C  92 ASN
C 134 HIS
D  76 GLN
D  89 GLN
D  90 GLN
D  92 ASN
D 353 ASN
E  76 GLN
E  89 GLN
E 326 ASN
F  76 GLN
F  90 GLN
F 326 ASN
F 353 ASN
G  76 GLN
G  89 GLN
G  90 GLN
G 134 HIS
G 326 ASN

Total number of N/Q/H flips: 31

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5886
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  20146  Z= 0.174
  Angle     :  0.592   7.741  27328  Z= 0.284
  Chirality :  0.039   0.126   3255
  Planarity :  0.004   0.038   3178
  Dihedral  : 14.451  89.927   4522
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 14.29 %
    Favored  : 82.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.17), residues: 2380
  helix:  1.55 (0.13), residues: 1533
  sheet: -1.21 (0.47), residues: 84
  loop : -2.33 (0.21), residues: 763

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP G  74 
 HIS   0.004   0.002   HIS D 134 
 PHE   0.011   0.001   PHE E 141 
 TYR   0.011   0.001   TYR E  10 
 ARG   0.005   0.000   ARG F 128 

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

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

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  472 residues out of total 2177 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 55
    poor density    : 417
  time to evaluate  : 2.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 GLU cc_start: 0.6413 (tt0) cc_final: 0.5801 (mm-30)
REVERT: A   13 SER cc_start: 0.7117 (t) cc_final: 0.6852 (p)
REVERT: A   35 ASP cc_start: 0.6701 (m-30) cc_final: 0.6475 (m-30)
REVERT: A   74 TRP cc_start: 0.7132 (t60) cc_final: 0.6829 (t-100)
REVERT: A  100 ASN cc_start: 0.7112 (m-40) cc_final: 0.6017 (t0)
REVERT: A  212 LYS cc_start: 0.5713 (mttt) cc_final: 0.5344 (mttp)
REVERT: A  222 ILE cc_start: 0.6982 (mm) cc_final: 0.6754 (mt)
REVERT: A  355 LYS cc_start: 0.5829 (ttpp) cc_final: 0.5457 (ttpp)
REVERT: B   35 ASP cc_start: 0.6575 (m-30) cc_final: 0.6079 (m-30)
REVERT: B   70 SER cc_start: 0.7310 (p) cc_final: 0.6968 (m)
REVERT: B   74 TRP cc_start: 0.7521 (t60) cc_final: 0.7058 (t-100)
REVERT: B   75 ARG cc_start: 0.7454 (mmm-85) cc_final: 0.7120 (mmt90)
REVERT: B  100 ASN cc_start: 0.6827 (m-40) cc_final: 0.5922 (t0)
REVERT: B  129 PHE cc_start: 0.8003 (m-80) cc_final: 0.7707 (m-80)
REVERT: B  201 LYS cc_start: 0.6678 (tppp) cc_final: 0.6450 (tppt)
REVERT: B  219 LEU cc_start: 0.6606 (mp) cc_final: 0.6402 (mp)
REVERT: B  254 ARG cc_start: 0.6892 (ttm110) cc_final: 0.6663 (ttm-80)
REVERT: B  262 GLN cc_start: 0.8220 (pt0) cc_final: 0.7971 (pt0)
REVERT: B  343 LYS cc_start: 0.5530 (OUTLIER) cc_final: 0.5184 (mmmt)
REVERT: C   35 ASP cc_start: 0.6311 (m-30) cc_final: 0.6028 (m-30)
REVERT: C   74 TRP cc_start: 0.7093 (t60) cc_final: 0.6683 (t-100)
REVERT: C  100 ASN cc_start: 0.7206 (m-40) cc_final: 0.6123 (t0)
REVERT: C  201 LYS cc_start: 0.6703 (tppp) cc_final: 0.6444 (tmmt)
REVERT: C  208 ASN cc_start: 0.5883 (t0) cc_final: 0.5587 (t0)
REVERT: C  222 ILE cc_start: 0.7046 (mm) cc_final: 0.6813 (mt)
REVERT: C  229 ILE cc_start: 0.7548 (mt) cc_final: 0.7211 (mm)
REVERT: C  254 ARG cc_start: 0.6661 (ttm110) cc_final: 0.6449 (ttm-80)
REVERT: C  299 PHE cc_start: 0.6121 (t80) cc_final: 0.5562 (t80)
REVERT: C  355 LYS cc_start: 0.5742 (mtpt) cc_final: 0.4950 (mmpt)
REVERT: D   36 LYS cc_start: 0.6505 (ttmm) cc_final: 0.6305 (ttmt)
REVERT: D   74 TRP cc_start: 0.7304 (t60) cc_final: 0.6955 (t-100)
REVERT: D   75 ARG cc_start: 0.7653 (mmm-85) cc_final: 0.7103 (mmt180)
REVERT: D  100 ASN cc_start: 0.7175 (m-40) cc_final: 0.6166 (t0)
REVERT: D  128 ARG cc_start: 0.7744 (tmm160) cc_final: 0.7539 (tmm160)
REVERT: D  219 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6168 (mp)
REVERT: D  222 ILE cc_start: 0.7129 (mm) cc_final: 0.6759 (mp)
REVERT: D  229 ILE cc_start: 0.7704 (mt) cc_final: 0.7450 (mm)
REVERT: D  262 GLN cc_start: 0.7965 (pt0) cc_final: 0.7749 (pt0)
REVERT: D  296 PHE cc_start: 0.7184 (m-80) cc_final: 0.6811 (m-80)
REVERT: D  355 LYS cc_start: 0.6568 (mtpp) cc_final: 0.5377 (mmpt)
REVERT: E   36 LYS cc_start: 0.6188 (ttmm) cc_final: 0.5500 (ttpt)
REVERT: E   74 TRP cc_start: 0.7299 (t60) cc_final: 0.7016 (t-100)
REVERT: E  100 ASN cc_start: 0.7464 (m-40) cc_final: 0.6254 (t0)
REVERT: E  139 LEU cc_start: 0.5754 (tp) cc_final: 0.5368 (tp)
REVERT: E  201 LYS cc_start: 0.6789 (tppp) cc_final: 0.6541 (tmmt)
REVERT: E  222 ILE cc_start: 0.7365 (mm) cc_final: 0.7012 (mt)
REVERT: E  229 ILE cc_start: 0.7602 (mt) cc_final: 0.7337 (mm)
REVERT: E  254 ARG cc_start: 0.6867 (ttm110) cc_final: 0.6624 (ttm-80)
REVERT: E  262 GLN cc_start: 0.8092 (pt0) cc_final: 0.7872 (pt0)
REVERT: E  296 PHE cc_start: 0.7100 (m-80) cc_final: 0.6795 (m-80)
REVERT: E  355 LYS cc_start: 0.6133 (mtpm) cc_final: 0.4989 (mmpt)
REVERT: F   31 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6854 (tt0)
REVERT: F   35 ASP cc_start: 0.6557 (m-30) cc_final: 0.6290 (m-30)
REVERT: F   36 LYS cc_start: 0.6319 (ttmt) cc_final: 0.6008 (ttmt)
REVERT: F  100 ASN cc_start: 0.7307 (m-40) cc_final: 0.6168 (t0)
REVERT: F  139 LEU cc_start: 0.5707 (tp) cc_final: 0.5427 (tp)
REVERT: F  201 LYS cc_start: 0.6562 (tppp) cc_final: 0.6326 (tmmt)
REVERT: F  222 ILE cc_start: 0.7173 (OUTLIER) cc_final: 0.6830 (mp)
REVERT: F  229 ILE cc_start: 0.7809 (mt) cc_final: 0.7527 (mm)
REVERT: F  243 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6662 (mt-10)
REVERT: G    5 GLN cc_start: 0.6043 (mt0) cc_final: 0.5714 (tp40)
REVERT: G   75 ARG cc_start: 0.7649 (mmt180) cc_final: 0.7328 (mmt180)
REVERT: G  100 ASN cc_start: 0.7363 (m-40) cc_final: 0.6139 (t0)
REVERT: G  222 ILE cc_start: 0.6908 (mm) cc_final: 0.6638 (mt)
REVERT: G  229 ILE cc_start: 0.7855 (mt) cc_final: 0.7563 (mp)
REVERT: G  296 PHE cc_start: 0.6979 (m-80) cc_final: 0.5984 (m-80)
REVERT: G  338 ASN cc_start: 0.6790 (m-40) cc_final: 0.6524 (m-40)
  outliers start: 55
  outliers final: 6
  residues processed: 454
  average time/residue: 1.0714
  time to fit residues: 560.2722
Evaluate side-chains
  350 residues out of total 2177 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 341
  time to evaluate  : 2.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue   91 LYS
Chi-restraints excluded: chain D residue   91 LYS
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  238 SER
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain F residue  222 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 238
   random chunks:
   chunk 120 optimal weight:    0.9980
   chunk 67 optimal weight:    6.9990
   chunk 179 optimal weight:   10.0000
   chunk 147 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 216 optimal weight:    3.9990
   chunk 233 optimal weight:   10.0000
   chunk 192 optimal weight:    2.9990
   chunk 214 optimal weight:    0.6980
   chunk 73 optimal weight:    2.9990
   chunk 173 optimal weight:    0.2980
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
C  89 GLN
C 274 GLN
D  89 GLN
D  92 ASN
D 326 ASN
E 326 ASN
E 338 ASN
F  89 GLN
F 326 ASN
F 338 ASN
G  92 ASN
G 326 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5978
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  20146  Z= 0.294
  Angle     :  0.654   7.630  27328  Z= 0.315
  Chirality :  0.041   0.156   3255
  Planarity :  0.004   0.039   3178
  Dihedral  : 13.537  85.244   4522
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 14.88 %
    Favored  : 79.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.18), residues: 2380
  helix:  1.54 (0.13), residues: 1568
  sheet: -0.22 (0.49), residues: 84
  loop : -2.11 (0.23), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP G  74 
 HIS   0.004   0.001   HIS E 134 
 PHE   0.019   0.002   PHE G  67 
 TYR   0.014   0.002   TYR G 230 
 ARG   0.007   0.001   ARG F 128 

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

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

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  451 residues out of total 2177 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 106
    poor density    : 345
  time to evaluate  : 2.175 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 GLU cc_start: 0.6471 (tt0) cc_final: 0.6213 (mt-10)
REVERT: A   35 ASP cc_start: 0.6889 (m-30) cc_final: 0.6657 (m-30)
REVERT: A   56 GLN cc_start: 0.7081 (tp-100) cc_final: 0.6331 (tt0)
REVERT: A   89 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.5939 (mp10)
REVERT: A  100 ASN cc_start: 0.7025 (m-40) cc_final: 0.6605 (m-40)
REVERT: A  343 LYS cc_start: 0.5677 (pttp) cc_final: 0.5093 (mmtp)
REVERT: B    9 GLU cc_start: 0.6605 (mt-10) cc_final: 0.5528 (mm-30)
REVERT: B   35 ASP cc_start: 0.6609 (m-30) cc_final: 0.6305 (m-30)
REVERT: B   70 SER cc_start: 0.7473 (p) cc_final: 0.6900 (m)
REVERT: B   74 TRP cc_start: 0.7316 (t60) cc_final: 0.6857 (t-100)
REVERT: B   89 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.6380 (mp10)
REVERT: B  100 ASN cc_start: 0.7011 (m-40) cc_final: 0.5862 (t0)
REVERT: B  129 PHE cc_start: 0.8073 (m-80) cc_final: 0.7716 (m-80)
REVERT: B  254 ARG cc_start: 0.6826 (ttm110) cc_final: 0.6543 (ttt180)
REVERT: B  262 GLN cc_start: 0.8142 (pt0) cc_final: 0.7903 (pt0)
REVERT: B  343 LYS cc_start: 0.6001 (OUTLIER) cc_final: 0.5633 (mmmt)
REVERT: C    9 GLU cc_start: 0.6732 (mt-10) cc_final: 0.5523 (mm-30)
REVERT: C   35 ASP cc_start: 0.6496 (m-30) cc_final: 0.6261 (m-30)
REVERT: C   74 TRP cc_start: 0.7126 (t60) cc_final: 0.6821 (t-100)
REVERT: C  100 ASN cc_start: 0.6892 (m-40) cc_final: 0.5720 (t0)
REVERT: C  201 LYS cc_start: 0.6932 (tppp) cc_final: 0.6558 (tmmt)
REVERT: C  222 ILE cc_start: 0.7031 (mm) cc_final: 0.6830 (mt)
REVERT: C  254 ARG cc_start: 0.6936 (ttm110) cc_final: 0.6734 (ttm-80)
REVERT: C  299 PHE cc_start: 0.6031 (t80) cc_final: 0.5456 (t80)
REVERT: C  338 ASN cc_start: 0.7209 (m-40) cc_final: 0.6568 (m110)
REVERT: C  345 TYR cc_start: 0.7320 (t80) cc_final: 0.6925 (t80)
REVERT: C  355 LYS cc_start: 0.5665 (OUTLIER) cc_final: 0.4922 (mmpt)
REVERT: D    9 GLU cc_start: 0.6137 (mt-10) cc_final: 0.5651 (mm-30)
REVERT: D   31 GLU cc_start: 0.6865 (tt0) cc_final: 0.6613 (tt0)
REVERT: D  100 ASN cc_start: 0.7118 (m-40) cc_final: 0.6129 (t0)
REVERT: D  111 TYR cc_start: 0.7319 (m-10) cc_final: 0.6407 (m-10)
REVERT: D  355 LYS cc_start: 0.6563 (mtpp) cc_final: 0.5214 (mmpt)
REVERT: E   36 LYS cc_start: 0.6318 (ttmm) cc_final: 0.5570 (ttpt)
REVERT: E   74 TRP cc_start: 0.7330 (t60) cc_final: 0.7023 (t-100)
REVERT: E   88 VAL cc_start: 0.7320 (OUTLIER) cc_final: 0.7037 (m)
REVERT: E   89 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.5867 (mp10)
REVERT: E  100 ASN cc_start: 0.7350 (m-40) cc_final: 0.6200 (t0)
REVERT: E  129 PHE cc_start: 0.8053 (m-80) cc_final: 0.7774 (m-80)
REVERT: E  139 LEU cc_start: 0.5948 (tp) cc_final: 0.5620 (tp)
REVERT: E  201 LYS cc_start: 0.6426 (tppp) cc_final: 0.6137 (tmmt)
REVERT: E  222 ILE cc_start: 0.7138 (mm) cc_final: 0.6888 (mt)
REVERT: E  254 ARG cc_start: 0.6720 (ttm110) cc_final: 0.6425 (ttm-80)
REVERT: E  262 GLN cc_start: 0.8101 (pt0) cc_final: 0.7859 (pt0)
REVERT: E  296 PHE cc_start: 0.7055 (m-80) cc_final: 0.5939 (m-80)
REVERT: E  343 LYS cc_start: 0.5673 (pttp) cc_final: 0.5173 (mmmt)
REVERT: E  355 LYS cc_start: 0.6298 (mtpm) cc_final: 0.5075 (mmpt)
REVERT: F    9 GLU cc_start: 0.6457 (mt-10) cc_final: 0.5401 (mm-30)
REVERT: F   31 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6797 (tt0)
REVERT: F   35 ASP cc_start: 0.6742 (m-30) cc_final: 0.6509 (m-30)
REVERT: F   36 LYS cc_start: 0.6459 (ttmt) cc_final: 0.6132 (ttmt)
REVERT: F  100 ASN cc_start: 0.7263 (m-40) cc_final: 0.6077 (t0)
REVERT: F  135 ILE cc_start: 0.6560 (OUTLIER) cc_final: 0.6214 (tt)
REVERT: F  222 ILE cc_start: 0.6823 (OUTLIER) cc_final: 0.6480 (mp)
REVERT: G   30 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7709 (mm)
REVERT: G   70 SER cc_start: 0.7280 (p) cc_final: 0.6904 (m)
REVERT: G   89 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.6379 (mp10)
REVERT: G  100 ASN cc_start: 0.6998 (m-40) cc_final: 0.5925 (t0)
REVERT: G  222 ILE cc_start: 0.6974 (mm) cc_final: 0.6749 (mt)
  outliers start: 106
  outliers final: 35
  residues processed: 417
  average time/residue: 1.0844
  time to fit residues: 521.2347
Evaluate side-chains
  360 residues out of total 2177 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 315
  time to evaluate  : 2.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 GLN
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain B residue    5 GLN
Chi-restraints excluded: chain B residue   68 SER
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain B residue  246 CYS
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain C residue    5 GLN
Chi-restraints excluded: chain C residue   56 GLN
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  246 CYS
Chi-restraints excluded: chain C residue  355 LYS
Chi-restraints excluded: chain D residue    5 GLN
Chi-restraints excluded: chain D residue   68 SER
Chi-restraints excluded: chain D residue   91 LYS
Chi-restraints excluded: chain D residue  214 ILE
Chi-restraints excluded: chain D residue  246 CYS
Chi-restraints excluded: chain E residue    5 GLN
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue   89 GLN
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  246 CYS
Chi-restraints excluded: chain E residue  338 ASN
Chi-restraints excluded: chain F residue    3 ILE
Chi-restraints excluded: chain F residue   89 GLN
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain F residue  135 ILE
Chi-restraints excluded: chain F residue  214 ILE
Chi-restraints excluded: chain F residue  222 ILE
Chi-restraints excluded: chain F residue  240 LEU
Chi-restraints excluded: chain F residue  246 CYS
Chi-restraints excluded: chain F residue  343 LYS
Chi-restraints excluded: chain G residue    3 ILE
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue   68 SER
Chi-restraints excluded: chain G residue   89 GLN
Chi-restraints excluded: chain G residue  246 CYS
Chi-restraints excluded: chain G residue  258 THR
Chi-restraints excluded: chain G residue  275 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 238
   random chunks:
   chunk 213 optimal weight:   10.0000
   chunk 162 optimal weight:    0.0970
   chunk 112 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 103 optimal weight:    0.0270
   chunk 145 optimal weight:    6.9990
   chunk 217 optimal weight:    2.9990
   chunk 230 optimal weight:    2.9990
   chunk 113 optimal weight:    0.6980
   chunk 205 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   overall best weight:    0.4836

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
C  89 GLN
D  89 GLN
D  92 ASN
D 134 HIS
E 134 HIS
E 338 ASN
F 134 HIS
G 100 ASN
G 353 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5929
moved from start:          0.3253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  20146  Z= 0.162
  Angle     :  0.550   7.137  27328  Z= 0.267
  Chirality :  0.038   0.123   3255
  Planarity :  0.004   0.037   3178
  Dihedral  : 12.689  87.636   4522
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 17.49 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.18), residues: 2380
  helix:  1.97 (0.13), residues: 1554
  sheet: -0.08 (0.57), residues: 84
  loop : -1.83 (0.24), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D  74 
 HIS   0.002   0.001   HIS D 134 
 PHE   0.014   0.001   PHE C  54 
 TYR   0.011   0.001   TYR D 230 
 ARG   0.006   0.000   ARG F 128 

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

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

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  402 residues out of total 2177 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 73
    poor density    : 329
  time to evaluate  : 2.021 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 GLU cc_start: 0.6297 (tt0) cc_final: 0.5830 (mm-30)
REVERT: A  100 ASN cc_start: 0.6865 (m-40) cc_final: 0.5785 (t0)
REVERT: A  212 LYS cc_start: 0.5718 (mttt) cc_final: 0.5402 (mttp)
REVERT: A  222 ILE cc_start: 0.7331 (mt) cc_final: 0.7119 (mt)
REVERT: A  243 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6924 (mt-10)
REVERT: A  343 LYS cc_start: 0.5487 (pttp) cc_final: 0.5074 (mmtp)
REVERT: B    5 GLN cc_start: 0.5916 (OUTLIER) cc_final: 0.5399 (tt0)
REVERT: B    9 GLU cc_start: 0.6593 (mt-10) cc_final: 0.5472 (mm-30)
REVERT: B   35 ASP cc_start: 0.6576 (m-30) cc_final: 0.6162 (m-30)
REVERT: B   70 SER cc_start: 0.7506 (p) cc_final: 0.6966 (m)
REVERT: B   74 TRP cc_start: 0.7295 (t60) cc_final: 0.6983 (t-100)
REVERT: B  100 ASN cc_start: 0.6764 (m-40) cc_final: 0.5715 (t0)
REVERT: B  254 ARG cc_start: 0.6873 (ttm110) cc_final: 0.6650 (ttm-80)
REVERT: B  262 GLN cc_start: 0.7954 (pt0) cc_final: 0.7713 (pt0)
REVERT: C    9 GLU cc_start: 0.6661 (mt-10) cc_final: 0.5515 (mm-30)
REVERT: C   35 ASP cc_start: 0.6352 (m-30) cc_final: 0.6130 (m-30)
REVERT: C   36 LYS cc_start: 0.6658 (ttmt) cc_final: 0.6373 (ttmt)
REVERT: C  100 ASN cc_start: 0.6996 (m-40) cc_final: 0.5765 (t0)
REVERT: C  201 LYS cc_start: 0.6841 (tppp) cc_final: 0.6509 (tmmt)
REVERT: C  254 ARG cc_start: 0.6818 (ttm110) cc_final: 0.6419 (mtt-85)
REVERT: C  264 GLN cc_start: 0.8624 (tp40) cc_final: 0.8177 (tp40)
REVERT: C  299 PHE cc_start: 0.6035 (t80) cc_final: 0.5538 (t80)
REVERT: C  345 TYR cc_start: 0.7315 (t80) cc_final: 0.6953 (t80)
REVERT: C  355 LYS cc_start: 0.5774 (mtpt) cc_final: 0.4811 (mmpt)
REVERT: D    9 GLU cc_start: 0.6183 (mt-10) cc_final: 0.5382 (mm-30)
REVERT: D   30 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7263 (mm)
REVERT: D   31 GLU cc_start: 0.7016 (tt0) cc_final: 0.6798 (tt0)
REVERT: D  100 ASN cc_start: 0.7054 (m-40) cc_final: 0.6045 (t0)
REVERT: D  222 ILE cc_start: 0.7323 (mt) cc_final: 0.7004 (mt)
REVERT: D  264 GLN cc_start: 0.8730 (tp40) cc_final: 0.8276 (mm-40)
REVERT: D  343 LYS cc_start: 0.4820 (pttt) cc_final: 0.4383 (mmmt)
REVERT: E   36 LYS cc_start: 0.6292 (ttmm) cc_final: 0.5589 (ttpt)
REVERT: E   56 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.5885 (pp30)
REVERT: E  100 ASN cc_start: 0.7277 (m-40) cc_final: 0.6060 (t0)
REVERT: E  139 LEU cc_start: 0.5940 (tp) cc_final: 0.5642 (tp)
REVERT: E  201 LYS cc_start: 0.6659 (tppp) cc_final: 0.6319 (tmmt)
REVERT: E  222 ILE cc_start: 0.7117 (mm) cc_final: 0.6857 (mt)
REVERT: E  262 GLN cc_start: 0.7995 (pt0) cc_final: 0.7776 (pt0)
REVERT: E  264 GLN cc_start: 0.8756 (tp40) cc_final: 0.8524 (tp40)
REVERT: E  296 PHE cc_start: 0.7171 (m-80) cc_final: 0.6844 (m-80)
REVERT: E  338 ASN cc_start: 0.6230 (OUTLIER) cc_final: 0.5994 (t160)
REVERT: E  343 LYS cc_start: 0.5218 (pttp) cc_final: 0.4825 (mmmt)
REVERT: E  355 LYS cc_start: 0.6156 (mtpm) cc_final: 0.4997 (mmpt)
REVERT: F    5 GLN cc_start: 0.5952 (tp40) cc_final: 0.5406 (tt0)
REVERT: F    9 GLU cc_start: 0.6291 (mt-10) cc_final: 0.5296 (mm-30)
REVERT: F   30 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7088 (mm)
REVERT: F   31 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6929 (tt0)
REVERT: F   35 ASP cc_start: 0.6640 (m-30) cc_final: 0.6380 (m-30)
REVERT: F   36 LYS cc_start: 0.6409 (ttmt) cc_final: 0.6102 (ttmt)
REVERT: F   56 GLN cc_start: 0.6844 (OUTLIER) cc_final: 0.6506 (mp10)
REVERT: F  100 ASN cc_start: 0.7158 (m-40) cc_final: 0.5993 (t0)
REVERT: F  122 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6401 (mp)
REVERT: F  222 ILE cc_start: 0.6896 (OUTLIER) cc_final: 0.6643 (mt)
REVERT: G    9 GLU cc_start: 0.5708 (OUTLIER) cc_final: 0.5370 (mm-30)
REVERT: G   56 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6797 (mp10)
REVERT: G   70 SER cc_start: 0.7315 (p) cc_final: 0.6964 (m)
REVERT: G  100 ASN cc_start: 0.7271 (m110) cc_final: 0.6058 (t0)
REVERT: G  222 ILE cc_start: 0.6897 (mm) cc_final: 0.6660 (mt)
REVERT: G  338 ASN cc_start: 0.7244 (m-40) cc_final: 0.7011 (m-40)
  outliers start: 73
  outliers final: 15
  residues processed: 385
  average time/residue: 1.1434
  time to fit residues: 503.7546
Evaluate side-chains
  331 residues out of total 2177 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 306
  time to evaluate  : 2.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 SER
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain B residue    5 GLN
Chi-restraints excluded: chain B residue  246 CYS
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue  246 CYS
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue  214 ILE
Chi-restraints excluded: chain D residue  246 CYS
Chi-restraints excluded: chain E residue   56 GLN
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  246 CYS
Chi-restraints excluded: chain E residue  338 ASN
Chi-restraints excluded: chain F residue   30 LEU
Chi-restraints excluded: chain F residue   56 GLN
Chi-restraints excluded: chain F residue  122 LEU
Chi-restraints excluded: chain F residue  222 ILE
Chi-restraints excluded: chain F residue  246 CYS
Chi-restraints excluded: chain G residue    3 ILE
Chi-restraints excluded: chain G residue    9 GLU
Chi-restraints excluded: chain G residue   56 GLN
Chi-restraints excluded: chain G residue  246 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 238
   random chunks:
   chunk 191 optimal weight:    0.8980
   chunk 130 optimal weight:    4.9990
   chunk 3 optimal weight:    7.9990
   chunk 171 optimal weight:    0.0070
   chunk 94 optimal weight:    0.0030
   chunk 196 optimal weight:    0.6980
   chunk 159 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 117 optimal weight:    5.9990
   chunk 206 optimal weight:    0.0070
   chunk 58 optimal weight:    4.9990
   overall best weight:    0.3226

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
A  92 ASN
A 264 GLN
C 353 ASN
D  89 GLN
D 264 GLN
E  89 GLN
E 338 ASN
F  89 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5900
moved from start:          0.3456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  20146  Z= 0.144
  Angle     :  0.527   7.118  27328  Z= 0.257
  Chirality :  0.038   0.123   3255
  Planarity :  0.004   0.037   3178
  Dihedral  : 11.953  86.927   4522
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 19.77 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.18), residues: 2380
  helix:  2.23 (0.13), residues: 1554
  sheet:  0.07 (0.60), residues: 84
  loop : -1.70 (0.24), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP G  74 
 HIS   0.002   0.001   HIS B 134 
 PHE   0.015   0.001   PHE F 141 
 TYR   0.009   0.001   TYR D 230 
 ARG   0.005   0.000   ARG E 217 

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

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

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  369 residues out of total 2177 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 59
    poor density    : 310
  time to evaluate  : 1.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 GLU cc_start: 0.6254 (tt0) cc_final: 0.5821 (mm-30)
REVERT: A  100 ASN cc_start: 0.6844 (m-40) cc_final: 0.5727 (t0)
REVERT: A  243 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6928 (mt-10)
REVERT: A  343 LYS cc_start: 0.5432 (pttp) cc_final: 0.4838 (mmtp)
REVERT: B    5 GLN cc_start: 0.5944 (OUTLIER) cc_final: 0.5486 (tt0)
REVERT: B    9 GLU cc_start: 0.6638 (mt-10) cc_final: 0.5532 (mm-30)
REVERT: B   35 ASP cc_start: 0.6504 (m-30) cc_final: 0.6283 (m-30)
REVERT: B   70 SER cc_start: 0.7483 (p) cc_final: 0.6965 (m)
REVERT: B   74 TRP cc_start: 0.7328 (t60) cc_final: 0.7077 (t-100)
REVERT: B  100 ASN cc_start: 0.6750 (m-40) cc_final: 0.5739 (t0)
REVERT: B  243 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6685 (mt-10)
REVERT: B  262 GLN cc_start: 0.7940 (pt0) cc_final: 0.7670 (pt0)
REVERT: B  349 LYS cc_start: 0.6109 (mmtt) cc_final: 0.5816 (mmtm)
REVERT: C    9 GLU cc_start: 0.6680 (mt-10) cc_final: 0.5625 (mm-30)
REVERT: C   35 ASP cc_start: 0.6306 (m-30) cc_final: 0.6045 (m-30)
REVERT: C   56 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6751 (mp10)
REVERT: C   89 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.6537 (mt0)
REVERT: C  100 ASN cc_start: 0.6966 (m-40) cc_final: 0.5728 (t0)
REVERT: C  201 LYS cc_start: 0.6793 (tppp) cc_final: 0.6476 (tmtt)
REVERT: C  243 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6877 (pt0)
REVERT: C  264 GLN cc_start: 0.8579 (tp40) cc_final: 0.8331 (tp40)
REVERT: C  299 PHE cc_start: 0.6011 (t80) cc_final: 0.5541 (t80)
REVERT: C  345 TYR cc_start: 0.7286 (t80) cc_final: 0.7080 (t80)
REVERT: C  355 LYS cc_start: 0.5915 (OUTLIER) cc_final: 0.4886 (mmpt)
REVERT: D    9 GLU cc_start: 0.6214 (mt-10) cc_final: 0.5390 (mm-30)
REVERT: D  100 ASN cc_start: 0.7034 (m-40) cc_final: 0.6008 (t0)
REVERT: D  111 TYR cc_start: 0.7249 (m-10) cc_final: 0.6690 (m-10)
REVERT: D  219 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.6190 (mp)
REVERT: D  222 ILE cc_start: 0.7315 (mt) cc_final: 0.6978 (mt)
REVERT: D  262 GLN cc_start: 0.7814 (pt0) cc_final: 0.7594 (pt0)
REVERT: D  264 GLN cc_start: 0.8529 (tp-100) cc_final: 0.8160 (mm-40)
REVERT: D  296 PHE cc_start: 0.7302 (m-80) cc_final: 0.6849 (m-80)
REVERT: D  343 LYS cc_start: 0.4528 (pttt) cc_final: 0.4045 (mmmt)
REVERT: E   36 LYS cc_start: 0.6176 (ttmm) cc_final: 0.5474 (ttpt)
REVERT: E   50 ILE cc_start: 0.7397 (mm) cc_final: 0.7146 (mt)
REVERT: E   56 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.5925 (pp30)
REVERT: E  100 ASN cc_start: 0.7231 (m-40) cc_final: 0.5998 (t0)
REVERT: E  139 LEU cc_start: 0.5704 (tp) cc_final: 0.5320 (tp)
REVERT: E  201 LYS cc_start: 0.6614 (tppp) cc_final: 0.6329 (tmmt)
REVERT: E  222 ILE cc_start: 0.7081 (mm) cc_final: 0.6841 (mt)
REVERT: E  262 GLN cc_start: 0.7905 (pt0) cc_final: 0.7666 (pt0)
REVERT: E  264 GLN cc_start: 0.8643 (tp40) cc_final: 0.8375 (tp40)
REVERT: E  296 PHE cc_start: 0.7167 (m-80) cc_final: 0.6840 (m-80)
REVERT: E  343 LYS cc_start: 0.4796 (pttp) cc_final: 0.4223 (mptm)
REVERT: F    5 GLN cc_start: 0.6032 (tp40) cc_final: 0.5517 (tt0)
REVERT: F    9 GLU cc_start: 0.6107 (mt-10) cc_final: 0.5211 (mm-30)
REVERT: F   30 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.7056 (mm)
REVERT: F   35 ASP cc_start: 0.6539 (m-30) cc_final: 0.6293 (m-30)
REVERT: F   36 LYS cc_start: 0.6310 (ttmt) cc_final: 0.6012 (ttmt)
REVERT: F   56 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6714 (mp10)
REVERT: F  100 ASN cc_start: 0.7169 (m-40) cc_final: 0.5923 (t0)
REVERT: F  122 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6386 (mp)
REVERT: F  222 ILE cc_start: 0.7040 (OUTLIER) cc_final: 0.6784 (mt)
REVERT: F  243 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6739 (mt-10)
REVERT: G    9 GLU cc_start: 0.5727 (OUTLIER) cc_final: 0.5438 (mm-30)
REVERT: G   70 SER cc_start: 0.7302 (p) cc_final: 0.6991 (m)
REVERT: G  100 ASN cc_start: 0.6875 (m110) cc_final: 0.5823 (t0)
REVERT: G  122 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6357 (mp)
REVERT: G  222 ILE cc_start: 0.6873 (mm) cc_final: 0.6646 (mt)
REVERT: G  338 ASN cc_start: 0.7157 (m-40) cc_final: 0.6894 (m-40)
  outliers start: 59
  outliers final: 17
  residues processed: 353
  average time/residue: 1.0528
  time to fit residues: 428.4730
Evaluate side-chains
  323 residues out of total 2177 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 294
  time to evaluate  : 2.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain B residue    5 GLN
Chi-restraints excluded: chain B residue  246 CYS
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain C residue    5 GLN
Chi-restraints excluded: chain C residue   56 GLN
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain C residue  246 CYS
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain C residue  355 LYS
Chi-restraints excluded: chain D residue  214 ILE
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  246 CYS
Chi-restraints excluded: chain E residue    5 GLN
Chi-restraints excluded: chain E residue   56 GLN
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  246 CYS
Chi-restraints excluded: chain E residue  258 THR
Chi-restraints excluded: chain F residue    3 ILE
Chi-restraints excluded: chain F residue   30 LEU
Chi-restraints excluded: chain F residue   56 GLN
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain F residue  122 LEU
Chi-restraints excluded: chain F residue  222 ILE
Chi-restraints excluded: chain F residue  246 CYS
Chi-restraints excluded: chain G residue    3 ILE
Chi-restraints excluded: chain G residue    9 GLU
Chi-restraints excluded: chain G residue  122 LEU
Chi-restraints excluded: chain G residue  246 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 238
   random chunks:
   chunk 77 optimal weight:    8.9990
   chunk 207 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 135 optimal weight:    0.7980
   chunk 56 optimal weight:    0.5980
   chunk 230 optimal weight:    0.9990
   chunk 191 optimal weight:    0.5980
   chunk 106 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 76 optimal weight:    0.6980
   chunk 120 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
B 134 HIS
C 353 ASN
D  89 GLN
E  89 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5922
moved from start:          0.3602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  20146  Z= 0.169
  Angle     :  0.533   7.187  27328  Z= 0.260
  Chirality :  0.038   0.151   3255
  Planarity :  0.004   0.038   3178
  Dihedral  : 11.800  85.316   4522
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 20.37 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.18), residues: 2380
  helix:  2.25 (0.13), residues: 1561
  sheet:  0.22 (0.61), residues: 84
  loop : -1.62 (0.24), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP G  74 
 HIS   0.003   0.001   HIS B 134 
 PHE   0.017   0.001   PHE D 141 
 TYR   0.009   0.001   TYR G 230 
 ARG   0.005   0.000   ARG E 217 

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

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

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  364 residues out of total 2177 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 65
    poor density    : 299
  time to evaluate  : 1.653 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 GLU cc_start: 0.6261 (tt0) cc_final: 0.5774 (mm-30)
REVERT: A   57 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6835 (pm20)
REVERT: A  100 ASN cc_start: 0.6903 (m-40) cc_final: 0.5787 (t0)
REVERT: A  122 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6282 (mp)
REVERT: A  219 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.6057 (mp)
REVERT: A  243 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6961 (mt-10)
REVERT: B    5 GLN cc_start: 0.5959 (OUTLIER) cc_final: 0.5469 (tt0)
REVERT: B    9 GLU cc_start: 0.6501 (mt-10) cc_final: 0.5416 (mm-30)
REVERT: B   35 ASP cc_start: 0.6498 (m-30) cc_final: 0.6283 (m-30)
REVERT: B   57 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6753 (pm20)
REVERT: B   70 SER cc_start: 0.7455 (p) cc_final: 0.6942 (m)
REVERT: B  100 ASN cc_start: 0.6799 (m-40) cc_final: 0.5719 (t0)
REVERT: B  243 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6739 (mt-10)
REVERT: B  262 GLN cc_start: 0.7913 (pt0) cc_final: 0.7657 (pt0)
REVERT: B  349 LYS cc_start: 0.6156 (mmtt) cc_final: 0.5858 (mmtm)
REVERT: C    9 GLU cc_start: 0.6668 (mt-10) cc_final: 0.5600 (mm-30)
REVERT: C   35 ASP cc_start: 0.6422 (m-30) cc_final: 0.6134 (m-30)
REVERT: C   56 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6769 (mp10)
REVERT: C   89 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.6521 (mt0)
REVERT: C  100 ASN cc_start: 0.7029 (m-40) cc_final: 0.5817 (t0)
REVERT: C  201 LYS cc_start: 0.6832 (tppp) cc_final: 0.6494 (tmtt)
REVERT: C  264 GLN cc_start: 0.8515 (tp40) cc_final: 0.8257 (tp40)
REVERT: C  299 PHE cc_start: 0.6033 (t80) cc_final: 0.5582 (t80)
REVERT: C  343 LYS cc_start: 0.5757 (OUTLIER) cc_final: 0.5473 (mptm)
REVERT: C  345 TYR cc_start: 0.7289 (t80) cc_final: 0.6972 (t80)
REVERT: D    9 GLU cc_start: 0.6190 (mt-10) cc_final: 0.5391 (mm-30)
REVERT: D  100 ASN cc_start: 0.7082 (m-40) cc_final: 0.6044 (t0)
REVERT: D  201 LYS cc_start: 0.6648 (tppt) cc_final: 0.6284 (tmmt)
REVERT: D  222 ILE cc_start: 0.7263 (mt) cc_final: 0.6928 (mt)
REVERT: D  262 GLN cc_start: 0.7791 (pt0) cc_final: 0.7555 (pt0)
REVERT: D  296 PHE cc_start: 0.7308 (m-80) cc_final: 0.6850 (m-80)
REVERT: D  343 LYS cc_start: 0.4697 (pttt) cc_final: 0.4168 (mmmt)
REVERT: E   36 LYS cc_start: 0.6188 (ttmm) cc_final: 0.5474 (ttpt)
REVERT: E   56 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.5997 (pp30)
REVERT: E  100 ASN cc_start: 0.7267 (m-40) cc_final: 0.6003 (t0)
REVERT: E  139 LEU cc_start: 0.5763 (tp) cc_final: 0.5450 (tp)
REVERT: E  201 LYS cc_start: 0.6266 (tppp) cc_final: 0.5955 (tmmt)
REVERT: E  222 ILE cc_start: 0.7093 (mm) cc_final: 0.6849 (mt)
REVERT: E  262 GLN cc_start: 0.7902 (pt0) cc_final: 0.7664 (pt0)
REVERT: E  264 GLN cc_start: 0.8668 (tp40) cc_final: 0.8368 (tp40)
REVERT: E  296 PHE cc_start: 0.7187 (m-80) cc_final: 0.6837 (m-80)
REVERT: F    5 GLN cc_start: 0.6062 (tp40) cc_final: 0.5526 (tt0)
REVERT: F    9 GLU cc_start: 0.6211 (mt-10) cc_final: 0.5130 (mm-30)
REVERT: F   30 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.7038 (mm)
REVERT: F   35 ASP cc_start: 0.6610 (m-30) cc_final: 0.6350 (m-30)
REVERT: F   36 LYS cc_start: 0.6301 (ttmt) cc_final: 0.6009 (ttmt)
REVERT: F   56 GLN cc_start: 0.6997 (OUTLIER) cc_final: 0.6742 (mp10)
REVERT: F  100 ASN cc_start: 0.7170 (m-40) cc_final: 0.5987 (t0)
REVERT: F  122 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6410 (mp)
REVERT: F  222 ILE cc_start: 0.6873 (OUTLIER) cc_final: 0.6619 (mt)
REVERT: G    9 GLU cc_start: 0.5613 (OUTLIER) cc_final: 0.5324 (mm-30)
REVERT: G   56 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6925 (mp10)
REVERT: G   70 SER cc_start: 0.7330 (p) cc_final: 0.6995 (m)
REVERT: G  100 ASN cc_start: 0.6925 (m110) cc_final: 0.5814 (t0)
REVERT: G  122 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6275 (mp)
REVERT: G  222 ILE cc_start: 0.6870 (mm) cc_final: 0.6645 (mt)
REVERT: G  338 ASN cc_start: 0.7313 (m-40) cc_final: 0.7056 (m-40)
  outliers start: 65
  outliers final: 24
  residues processed: 343
  average time/residue: 1.0544
  time to fit residues: 417.1856
Evaluate side-chains
  331 residues out of total 2177 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 291
  time to evaluate  : 2.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 ILE
Chi-restraints excluded: chain A residue    5 GLN
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain B residue    3 ILE
Chi-restraints excluded: chain B residue    5 GLN
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue  246 CYS
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  339 ILE
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue    5 GLN
Chi-restraints excluded: chain C residue   56 GLN
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain C residue   91 LYS
Chi-restraints excluded: chain C residue  246 CYS
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain D residue    5 GLN
Chi-restraints excluded: chain D residue  214 ILE
Chi-restraints excluded: chain D residue  246 CYS
Chi-restraints excluded: chain E residue    5 GLN
Chi-restraints excluded: chain E residue   56 GLN
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  246 CYS
Chi-restraints excluded: chain E residue  258 THR
Chi-restraints excluded: chain F residue   30 LEU
Chi-restraints excluded: chain F residue   56 GLN
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain F residue  122 LEU
Chi-restraints excluded: chain F residue  222 ILE
Chi-restraints excluded: chain F residue  246 CYS
Chi-restraints excluded: chain F residue  343 LYS
Chi-restraints excluded: chain G residue    3 ILE
Chi-restraints excluded: chain G residue    9 GLU
Chi-restraints excluded: chain G residue   56 GLN
Chi-restraints excluded: chain G residue  122 LEU
Chi-restraints excluded: chain G residue  246 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 238
   random chunks:
   chunk 222 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 131 optimal weight:    5.9990
   chunk 168 optimal weight:    3.9990
   chunk 130 optimal weight:    6.9990
   chunk 193 optimal weight:    0.9980
   chunk 128 optimal weight:    0.8980
   chunk 229 optimal weight:    4.9990
   chunk 143 optimal weight:    1.9990
   chunk 139 optimal weight:    0.0370
   chunk 105 optimal weight:    0.9980
   overall best weight:    0.9860

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
D  89 GLN
E  89 GLN
F  89 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5949
moved from start:          0.3757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  20146  Z= 0.210
  Angle     :  0.563   7.382  27328  Z= 0.274
  Chirality :  0.039   0.146   3255
  Planarity :  0.004   0.039   3178
  Dihedral  : 11.829  78.234   4522
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.48 %
    Favored  : 75.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.18), residues: 2380
  helix:  2.20 (0.13), residues: 1554
  sheet: -0.25 (0.59), residues: 91
  loop : -1.50 (0.25), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP F  74 
 HIS   0.002   0.001   HIS F 106 
 PHE   0.017   0.002   PHE F 141 
 TYR   0.011   0.001   TYR G 230 
 ARG   0.005   0.000   ARG E 217 

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

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

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  378 residues out of total 2177 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 70
    poor density    : 308
  time to evaluate  : 2.048 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 GLU cc_start: 0.6173 (tt0) cc_final: 0.5641 (mm-30)
REVERT: A   30 LEU cc_start: 0.7404 (mt) cc_final: 0.7197 (mm)
REVERT: A   57 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6958 (pm20)
REVERT: A  100 ASN cc_start: 0.6955 (m-40) cc_final: 0.6489 (m-40)
REVERT: A  122 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6308 (mp)
REVERT: A  243 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6918 (mt-10)
REVERT: B    5 GLN cc_start: 0.5951 (OUTLIER) cc_final: 0.5438 (tt0)
REVERT: B    9 GLU cc_start: 0.6573 (mt-10) cc_final: 0.5441 (mm-30)
REVERT: B   35 ASP cc_start: 0.6567 (m-30) cc_final: 0.6344 (m-30)
REVERT: B   57 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6676 (pm20)
REVERT: B   70 SER cc_start: 0.7506 (p) cc_final: 0.6929 (m)
REVERT: B  100 ASN cc_start: 0.6902 (m-40) cc_final: 0.5796 (t0)
REVERT: B  129 PHE cc_start: 0.7898 (m-80) cc_final: 0.7607 (m-80)
REVERT: B  243 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6911 (mt-10)
REVERT: B  254 ARG cc_start: 0.6992 (ttm110) cc_final: 0.6728 (mtt-85)
REVERT: B  262 GLN cc_start: 0.7959 (pt0) cc_final: 0.7711 (pt0)
REVERT: B  299 PHE cc_start: 0.6211 (t80) cc_final: 0.5588 (t80)
REVERT: C    9 GLU cc_start: 0.6702 (mt-10) cc_final: 0.5599 (mm-30)
REVERT: C   35 ASP cc_start: 0.6482 (m-30) cc_final: 0.6188 (m-30)
REVERT: C   56 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6787 (mp10)
REVERT: C   89 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.6645 (mt0)
REVERT: C  100 ASN cc_start: 0.7044 (m-40) cc_final: 0.5777 (t0)
REVERT: C  201 LYS cc_start: 0.6868 (tppp) cc_final: 0.6529 (tmmt)
REVERT: C  264 GLN cc_start: 0.8601 (tp40) cc_final: 0.8054 (tp40)
REVERT: C  299 PHE cc_start: 0.6125 (t80) cc_final: 0.5615 (t80)
REVERT: C  343 LYS cc_start: 0.5957 (OUTLIER) cc_final: 0.5657 (mptm)
REVERT: C  345 TYR cc_start: 0.7353 (t80) cc_final: 0.7013 (t80)
REVERT: C  355 LYS cc_start: 0.5917 (mtpt) cc_final: 0.4853 (mmpt)
REVERT: D    9 GLU cc_start: 0.6034 (mt-10) cc_final: 0.5241 (mm-30)
REVERT: D  100 ASN cc_start: 0.7163 (m-40) cc_final: 0.6091 (t0)
REVERT: D  111 TYR cc_start: 0.7324 (m-10) cc_final: 0.6618 (m-10)
REVERT: D  222 ILE cc_start: 0.7291 (mt) cc_final: 0.6954 (mt)
REVERT: D  343 LYS cc_start: 0.4936 (pttt) cc_final: 0.4354 (mmmt)
REVERT: E   36 LYS cc_start: 0.6318 (ttmm) cc_final: 0.5579 (ttpt)
REVERT: E   56 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6457 (mt0)
REVERT: E  100 ASN cc_start: 0.7065 (m-40) cc_final: 0.5904 (t0)
REVERT: E  139 LEU cc_start: 0.5912 (tp) cc_final: 0.5640 (tp)
REVERT: E  201 LYS cc_start: 0.6462 (tppp) cc_final: 0.6114 (tmmt)
REVERT: E  222 ILE cc_start: 0.7107 (mm) cc_final: 0.6854 (mt)
REVERT: E  262 GLN cc_start: 0.7957 (pt0) cc_final: 0.7736 (pt0)
REVERT: E  296 PHE cc_start: 0.7179 (m-80) cc_final: 0.6890 (m-80)
REVERT: E  352 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.6200 (tt0)
REVERT: F    5 GLN cc_start: 0.6028 (OUTLIER) cc_final: 0.5442 (tt0)
REVERT: F    9 GLU cc_start: 0.6195 (mt-10) cc_final: 0.5114 (mm-30)
REVERT: F   30 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7108 (mm)
REVERT: F   35 ASP cc_start: 0.6718 (m-30) cc_final: 0.6347 (m-30)
REVERT: F   36 LYS cc_start: 0.6502 (ttmt) cc_final: 0.6247 (ttmt)
REVERT: F   56 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6788 (mp10)
REVERT: F  100 ASN cc_start: 0.7233 (m-40) cc_final: 0.6079 (t0)
REVERT: F  122 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6385 (mp)
REVERT: F  222 ILE cc_start: 0.6763 (OUTLIER) cc_final: 0.6503 (mt)
REVERT: F  294 THR cc_start: 0.7126 (m) cc_final: 0.6921 (p)
REVERT: F  299 PHE cc_start: 0.6226 (t80) cc_final: 0.5653 (t80)
REVERT: F  326 ASN cc_start: 0.6890 (OUTLIER) cc_final: 0.6203 (p0)
REVERT: F  343 LYS cc_start: 0.5349 (OUTLIER) cc_final: 0.4724 (mppt)
REVERT: G    9 GLU cc_start: 0.5688 (OUTLIER) cc_final: 0.5397 (mm-30)
REVERT: G   56 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6774 (mp10)
REVERT: G   70 SER cc_start: 0.7273 (p) cc_final: 0.6915 (m)
REVERT: G  100 ASN cc_start: 0.7077 (m110) cc_final: 0.5909 (t0)
REVERT: G  122 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6345 (mp)
REVERT: G  222 ILE cc_start: 0.6881 (mm) cc_final: 0.6656 (mt)
REVERT: G  338 ASN cc_start: 0.7430 (m-40) cc_final: 0.7190 (m-40)
REVERT: G  352 GLU cc_start: 0.6792 (tm-30) cc_final: 0.6541 (tp30)
  outliers start: 70
  outliers final: 26
  residues processed: 357
  average time/residue: 1.0947
  time to fit residues: 449.7243
Evaluate side-chains
  346 residues out of total 2177 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 301
  time to evaluate  : 2.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 ILE
Chi-restraints excluded: chain A residue    5 GLN
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain B residue    5 GLN
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue  246 CYS
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  339 ILE
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue    5 GLN
Chi-restraints excluded: chain C residue   56 GLN
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain C residue   91 LYS
Chi-restraints excluded: chain C residue  246 CYS
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain D residue    5 GLN
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue  214 ILE
Chi-restraints excluded: chain D residue  246 CYS
Chi-restraints excluded: chain E residue    5 GLN
Chi-restraints excluded: chain E residue   56 GLN
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  246 CYS
Chi-restraints excluded: chain E residue  258 THR
Chi-restraints excluded: chain E residue  352 GLU
Chi-restraints excluded: chain F residue    3 ILE
Chi-restraints excluded: chain F residue    5 GLN
Chi-restraints excluded: chain F residue   30 LEU
Chi-restraints excluded: chain F residue   56 GLN
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain F residue  122 LEU
Chi-restraints excluded: chain F residue  222 ILE
Chi-restraints excluded: chain F residue  246 CYS
Chi-restraints excluded: chain F residue  326 ASN
Chi-restraints excluded: chain F residue  343 LYS
Chi-restraints excluded: chain G residue    3 ILE
Chi-restraints excluded: chain G residue    9 GLU
Chi-restraints excluded: chain G residue   56 GLN
Chi-restraints excluded: chain G residue  122 LEU
Chi-restraints excluded: chain G residue  246 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 238
   random chunks:
   chunk 141 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   chunk 137 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 145 optimal weight:    5.9990
   chunk 156 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 180 optimal weight:    0.5980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
D  89 GLN
E  89 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5940
moved from start:          0.3876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  20146  Z= 0.192
  Angle     :  0.547   7.575  27328  Z= 0.266
  Chirality :  0.038   0.131   3255
  Planarity :  0.004   0.039   3178
  Dihedral  : 11.535  72.554   4522
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 20.91 %
    Favored  : 75.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.18), residues: 2380
  helix:  2.16 (0.13), residues: 1568
  sheet: -0.19 (0.58), residues: 91
  loop : -1.43 (0.25), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP F  74 
 HIS   0.002   0.001   HIS F 106 
 PHE   0.019   0.002   PHE G 141 
 TYR   0.011   0.001   TYR F 230 
 ARG   0.006   0.000   ARG E 217 

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

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

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  364 residues out of total 2177 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 63
    poor density    : 301
  time to evaluate  : 1.917 
Fit side-chains
REVERT: A    9 GLU cc_start: 0.6144 (tt0) cc_final: 0.5644 (mm-30)
REVERT: A   57 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6968 (pm20)
REVERT: A  100 ASN cc_start: 0.6962 (m-40) cc_final: 0.6440 (m-40)
REVERT: A  122 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6299 (mp)
REVERT: A  243 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6898 (mt-10)
REVERT: B    5 GLN cc_start: 0.5987 (OUTLIER) cc_final: 0.5447 (tt0)
REVERT: B    9 GLU cc_start: 0.6540 (mt-10) cc_final: 0.5405 (mm-30)
REVERT: B   35 ASP cc_start: 0.6621 (m-30) cc_final: 0.6346 (m-30)
REVERT: B   57 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6809 (pm20)
REVERT: B   70 SER cc_start: 0.7542 (p) cc_final: 0.6934 (m)
REVERT: B  100 ASN cc_start: 0.6898 (m-40) cc_final: 0.5785 (t0)
REVERT: B  128 ARG cc_start: 0.7690 (ttp-170) cc_final: 0.7301 (ttp-170)
REVERT: B  129 PHE cc_start: 0.7916 (m-80) cc_final: 0.7581 (m-80)
REVERT: B  243 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6822 (mt-10)
REVERT: B  254 ARG cc_start: 0.6929 (ttm110) cc_final: 0.6653 (mtt-85)
REVERT: B  262 GLN cc_start: 0.7982 (pt0) cc_final: 0.7728 (pt0)
REVERT: B  299 PHE cc_start: 0.6149 (t80) cc_final: 0.5520 (t80)
REVERT: B  349 LYS cc_start: 0.6233 (mmtt) cc_final: 0.6009 (mmtm)
REVERT: C    9 GLU cc_start: 0.6736 (mt-10) cc_final: 0.5605 (mm-30)
REVERT: C   35 ASP cc_start: 0.6464 (m-30) cc_final: 0.6232 (m-30)
REVERT: C   56 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6844 (mp10)
REVERT: C   89 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.6628 (mt0)
REVERT: C  100 ASN cc_start: 0.7141 (m-40) cc_final: 0.5880 (t0)
REVERT: C  201 LYS cc_start: 0.6865 (tppp) cc_final: 0.6534 (tmmt)
REVERT: C  264 GLN cc_start: 0.8532 (tp40) cc_final: 0.7964 (tp40)
REVERT: C  299 PHE cc_start: 0.6080 (t80) cc_final: 0.5560 (t80)
REVERT: C  343 LYS cc_start: 0.5940 (OUTLIER) cc_final: 0.5667 (mptm)
REVERT: C  345 TYR cc_start: 0.7243 (t80) cc_final: 0.6924 (t80)
REVERT: C  355 LYS cc_start: 0.5951 (mtpt) cc_final: 0.4904 (mmpt)
REVERT: D    9 GLU cc_start: 0.6114 (mt-10) cc_final: 0.5310 (mm-30)
REVERT: D  100 ASN cc_start: 0.7064 (m-40) cc_final: 0.5996 (t0)
REVERT: D  222 ILE cc_start: 0.7265 (mt) cc_final: 0.6927 (mt)
REVERT: D  262 GLN cc_start: 0.7788 (pt0) cc_final: 0.7546 (pt0)
REVERT: D  343 LYS cc_start: 0.4919 (pttt) cc_final: 0.4264 (mmmt)
REVERT: E   36 LYS cc_start: 0.6312 (ttmm) cc_final: 0.5569 (ttpt)
REVERT: E   56 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.6504 (mt0)
REVERT: E  100 ASN cc_start: 0.7214 (m-40) cc_final: 0.5974 (t0)
REVERT: E  139 LEU cc_start: 0.5901 (tp) cc_final: 0.5613 (tp)
REVERT: E  201 LYS cc_start: 0.6480 (tppp) cc_final: 0.6113 (tmmt)
REVERT: E  222 ILE cc_start: 0.6966 (mm) cc_final: 0.6711 (mt)
REVERT: E  262 GLN cc_start: 0.7973 (pt0) cc_final: 0.7748 (pt0)
REVERT: E  296 PHE cc_start: 0.7157 (m-80) cc_final: 0.6894 (m-80)
REVERT: F    5 GLN cc_start: 0.6026 (OUTLIER) cc_final: 0.5456 (tt0)
REVERT: F    9 GLU cc_start: 0.6238 (mt-10) cc_final: 0.5140 (mm-30)
REVERT: F   30 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7172 (mm)
REVERT: F   35 ASP cc_start: 0.6697 (m-30) cc_final: 0.6315 (m-30)
REVERT: F   36 LYS cc_start: 0.6531 (ttmt) cc_final: 0.6200 (ttmt)
REVERT: F   56 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6818 (mp10)
REVERT: F  100 ASN cc_start: 0.7321 (m-40) cc_final: 0.6114 (t0)
REVERT: F  122 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6389 (mp)
REVERT: F  222 ILE cc_start: 0.6761 (OUTLIER) cc_final: 0.6504 (mt)
REVERT: F  299 PHE cc_start: 0.6192 (t80) cc_final: 0.5625 (t80)
REVERT: F  326 ASN cc_start: 0.6916 (OUTLIER) cc_final: 0.6230 (p0)
REVERT: F  343 LYS cc_start: 0.5473 (OUTLIER) cc_final: 0.4370 (mptp)
REVERT: G    9 GLU cc_start: 0.5687 (OUTLIER) cc_final: 0.5390 (mm-30)
REVERT: G   56 GLN cc_start: 0.7052 (OUTLIER) cc_final: 0.6783 (mp10)
REVERT: G   70 SER cc_start: 0.7288 (p) cc_final: 0.6922 (m)
REVERT: G  100 ASN cc_start: 0.7372 (m110) cc_final: 0.6106 (t0)
REVERT: G  222 ILE cc_start: 0.6880 (mm) cc_final: 0.6658 (mt)
REVERT: G  338 ASN cc_start: 0.7423 (m-40) cc_final: 0.7151 (m-40)
REVERT: G  352 GLU cc_start: 0.6778 (tm-30) cc_final: 0.6515 (tp30)
  outliers start: 63
  outliers final: 27
  residues processed: 344
  average time/residue: 1.0994
  time to fit residues: 434.5488
Evaluate side-chains
  345 residues out of total 2177 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 301
  time to evaluate  : 2.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 ILE
Chi-restraints excluded: chain A residue    5 GLN
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain B residue    3 ILE
Chi-restraints excluded: chain B residue    5 GLN
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue  246 CYS
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue    5 GLN
Chi-restraints excluded: chain C residue   56 GLN
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain C residue   91 LYS
Chi-restraints excluded: chain C residue  246 CYS
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain D residue    3 ILE
Chi-restraints excluded: chain D residue    5 GLN
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue  214 ILE
Chi-restraints excluded: chain D residue  246 CYS
Chi-restraints excluded: chain E residue    5 GLN
Chi-restraints excluded: chain E residue   56 GLN
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  246 CYS
Chi-restraints excluded: chain E residue  258 THR
Chi-restraints excluded: chain E residue  339 ILE
Chi-restraints excluded: chain F residue    3 ILE
Chi-restraints excluded: chain F residue    5 GLN
Chi-restraints excluded: chain F residue   30 LEU
Chi-restraints excluded: chain F residue   56 GLN
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain F residue  122 LEU
Chi-restraints excluded: chain F residue  222 ILE
Chi-restraints excluded: chain F residue  246 CYS
Chi-restraints excluded: chain F residue  326 ASN
Chi-restraints excluded: chain F residue  343 LYS
Chi-restraints excluded: chain G residue    3 ILE
Chi-restraints excluded: chain G residue    9 GLU
Chi-restraints excluded: chain G residue   56 GLN
Chi-restraints excluded: chain G residue  246 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 238
   random chunks:
   chunk 208 optimal weight:    0.8980
   chunk 219 optimal weight:    5.9990
   chunk 200 optimal weight:    3.9990
   chunk 213 optimal weight:   10.0000
   chunk 128 optimal weight:    1.9990
   chunk 93 optimal weight:    4.9990
   chunk 167 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9990
   chunk 193 optimal weight:    0.9980
   chunk 202 optimal weight:    5.9990
   chunk 140 optimal weight:    0.3980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
E  89 GLN
F  89 GLN
G 353 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5956
moved from start:          0.3978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  20146  Z= 0.221
  Angle     :  0.569   7.572  27328  Z= 0.277
  Chirality :  0.039   0.143   3255
  Planarity :  0.004   0.040   3178
  Dihedral  : 11.555  68.116   4522
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 20.97 %
    Favored  : 75.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.18), residues: 2380
  helix:  2.13 (0.13), residues: 1561
  sheet: -0.18 (0.58), residues: 91
  loop : -1.46 (0.25), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP F  74 
 HIS   0.002   0.001   HIS F 106 
 PHE   0.020   0.002   PHE B 141 
 TYR   0.012   0.002   TYR F 230 
 ARG   0.006   0.000   ARG E 217 

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

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

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  371 residues out of total 2177 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 63
    poor density    : 308
  time to evaluate  : 2.055 
Fit side-chains
REVERT: A    9 GLU cc_start: 0.6258 (tt0) cc_final: 0.5686 (mm-30)
REVERT: A   31 GLU cc_start: 0.6708 (tt0) cc_final: 0.6459 (tt0)
REVERT: A   57 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7004 (pm20)
REVERT: A  100 ASN cc_start: 0.6997 (m-40) cc_final: 0.6500 (m-40)
REVERT: A  122 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6308 (mp)
REVERT: A  243 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6952 (mt-10)
REVERT: B    5 GLN cc_start: 0.5967 (OUTLIER) cc_final: 0.5426 (tt0)
REVERT: B    9 GLU cc_start: 0.6618 (mt-10) cc_final: 0.5486 (mm-30)
REVERT: B   35 ASP cc_start: 0.6626 (m-30) cc_final: 0.6351 (m-30)
REVERT: B   57 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6829 (pm20)
REVERT: B   70 SER cc_start: 0.7504 (p) cc_final: 0.6920 (m)
REVERT: B  100 ASN cc_start: 0.6916 (m-40) cc_final: 0.5803 (t0)
REVERT: B  128 ARG cc_start: 0.7700 (ttp-170) cc_final: 0.7305 (ttp-170)
REVERT: B  129 PHE cc_start: 0.7937 (m-80) cc_final: 0.7606 (m-80)
REVERT: B  243 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7003 (mt-10)
REVERT: B  254 ARG cc_start: 0.6919 (ttm110) cc_final: 0.6619 (mtt-85)
REVERT: B  262 GLN cc_start: 0.7982 (pt0) cc_final: 0.7722 (pt0)
REVERT: B  299 PHE cc_start: 0.6210 (t80) cc_final: 0.5589 (t80)
REVERT: B  349 LYS cc_start: 0.6225 (mmtt) cc_final: 0.5996 (mmtm)
REVERT: C    9 GLU cc_start: 0.6705 (mt-10) cc_final: 0.5607 (mm-30)
REVERT: C   56 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6883 (mp10)
REVERT: C   89 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.6665 (mt0)
REVERT: C  100 ASN cc_start: 0.7010 (m-40) cc_final: 0.5740 (t0)
REVERT: C  201 LYS cc_start: 0.6888 (tppp) cc_final: 0.6554 (tmmt)
REVERT: C  299 PHE cc_start: 0.6019 (t80) cc_final: 0.5490 (t80)
REVERT: C  345 TYR cc_start: 0.7294 (t80) cc_final: 0.6854 (t80)
REVERT: C  355 LYS cc_start: 0.5998 (mtpt) cc_final: 0.5042 (mmpt)
REVERT: D    9 GLU cc_start: 0.5994 (mt-10) cc_final: 0.5178 (mm-30)
REVERT: D  100 ASN cc_start: 0.7116 (m-40) cc_final: 0.6046 (t0)
REVERT: D  111 TYR cc_start: 0.7314 (m-10) cc_final: 0.6590 (m-10)
REVERT: D  343 LYS cc_start: 0.4953 (pttt) cc_final: 0.4313 (mmmt)
REVERT: E   36 LYS cc_start: 0.6321 (ttmm) cc_final: 0.5582 (ttpt)
REVERT: E   56 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6529 (mt0)
REVERT: E  100 ASN cc_start: 0.7286 (m-40) cc_final: 0.6085 (t0)
REVERT: E  128 ARG cc_start: 0.7419 (ttp-170) cc_final: 0.7182 (ttp-170)
REVERT: E  139 LEU cc_start: 0.5906 (tp) cc_final: 0.5632 (tp)
REVERT: E  201 LYS cc_start: 0.6493 (tppp) cc_final: 0.6115 (tmmt)
REVERT: E  222 ILE cc_start: 0.6978 (mm) cc_final: 0.6742 (mt)
REVERT: E  262 GLN cc_start: 0.8010 (pt0) cc_final: 0.7792 (pt0)
REVERT: E  296 PHE cc_start: 0.7150 (m-80) cc_final: 0.6934 (m-80)
REVERT: E  349 LYS cc_start: 0.6088 (OUTLIER) cc_final: 0.5880 (tptp)
REVERT: F    5 GLN cc_start: 0.6043 (OUTLIER) cc_final: 0.5467 (tt0)
REVERT: F    9 GLU cc_start: 0.6265 (mt-10) cc_final: 0.5162 (mm-30)
REVERT: F   30 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7142 (mm)
REVERT: F   35 ASP cc_start: 0.6706 (m-30) cc_final: 0.6441 (m-30)
REVERT: F   36 LYS cc_start: 0.6481 (ttmt) cc_final: 0.6206 (ttmt)
REVERT: F   56 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.6710 (mp10)
REVERT: F   89 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7528 (mm-40)
REVERT: F  100 ASN cc_start: 0.7347 (m-40) cc_final: 0.6081 (t0)
REVERT: F  122 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6383 (mp)
REVERT: F  299 PHE cc_start: 0.6236 (t80) cc_final: 0.5650 (t80)
REVERT: F  326 ASN cc_start: 0.6808 (OUTLIER) cc_final: 0.6150 (p0)
REVERT: F  343 LYS cc_start: 0.5498 (OUTLIER) cc_final: 0.4408 (mptp)
REVERT: G   70 SER cc_start: 0.7270 (p) cc_final: 0.6903 (m)
REVERT: G   89 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.5906 (mp10)
REVERT: G  100 ASN cc_start: 0.7304 (m110) cc_final: 0.6139 (t0)
REVERT: G  352 GLU cc_start: 0.6793 (tm-30) cc_final: 0.6539 (tp30)
  outliers start: 63
  outliers final: 31
  residues processed: 349
  average time/residue: 1.1105
  time to fit residues: 445.0416
Evaluate side-chains
  350 residues out of total 2177 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 303
  time to evaluate  : 2.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 ILE
Chi-restraints excluded: chain A residue    5 GLN
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain B residue    3 ILE
Chi-restraints excluded: chain B residue    5 GLN
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue  246 CYS
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  339 ILE
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue    5 GLN
Chi-restraints excluded: chain C residue   56 GLN
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain C residue   91 LYS
Chi-restraints excluded: chain C residue  246 CYS
Chi-restraints excluded: chain D residue    3 ILE
Chi-restraints excluded: chain D residue    5 GLN
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue  214 ILE
Chi-restraints excluded: chain D residue  246 CYS
Chi-restraints excluded: chain E residue    5 GLN
Chi-restraints excluded: chain E residue   56 GLN
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  246 CYS
Chi-restraints excluded: chain E residue  258 THR
Chi-restraints excluded: chain E residue  339 ILE
Chi-restraints excluded: chain E residue  349 LYS
Chi-restraints excluded: chain F residue    3 ILE
Chi-restraints excluded: chain F residue    5 GLN
Chi-restraints excluded: chain F residue   30 LEU
Chi-restraints excluded: chain F residue   56 GLN
Chi-restraints excluded: chain F residue   89 GLN
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain F residue  122 LEU
Chi-restraints excluded: chain F residue  222 ILE
Chi-restraints excluded: chain F residue  246 CYS
Chi-restraints excluded: chain F residue  326 ASN
Chi-restraints excluded: chain F residue  343 LYS
Chi-restraints excluded: chain G residue    3 ILE
Chi-restraints excluded: chain G residue    9 GLU
Chi-restraints excluded: chain G residue   89 GLN
Chi-restraints excluded: chain G residue  246 CYS
Chi-restraints excluded: chain G residue  258 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 238
   random chunks:
   chunk 226 optimal weight:    3.9990
   chunk 137 optimal weight:    1.9990
   chunk 107 optimal weight:    0.5980
   chunk 157 optimal weight:    3.9990
   chunk 237 optimal weight:    1.9990
   chunk 218 optimal weight:   10.0000
   chunk 188 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 145 optimal weight:    3.9990
   chunk 115 optimal weight:    0.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    1.3188

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
A 274 GLN
** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  89 GLN
E 353 ASN
F  89 GLN
G 353 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5968
moved from start:          0.4082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  20146  Z= 0.250
  Angle     :  0.589   8.270  27328  Z= 0.286
  Chirality :  0.040   0.160   3255
  Planarity :  0.004   0.040   3178
  Dihedral  : 11.653  66.333   4522
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 21.51 %
    Favored  : 75.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.18), residues: 2380
  helix:  2.02 (0.13), residues: 1568
  sheet: -0.15 (0.57), residues: 91
  loop : -1.47 (0.25), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.003   TRP F  74 
 HIS   0.003   0.001   HIS F 106 
 PHE   0.021   0.002   PHE G 141 
 TYR   0.012   0.002   TYR D 230 
 ARG   0.007   0.001   ARG C 254 

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

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

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  353 residues out of total 2177 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 55
    poor density    : 298
  time to evaluate  : 1.947 
Fit side-chains
REVERT: A    9 GLU cc_start: 0.6227 (tt0) cc_final: 0.5684 (mm-30)
REVERT: A   31 GLU cc_start: 0.6957 (tt0) cc_final: 0.6718 (tt0)
REVERT: A   56 GLN cc_start: 0.6989 (tp-100) cc_final: 0.6265 (mt0)
REVERT: A   57 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7080 (pm20)
REVERT: A   89 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7268 (mt0)
REVERT: A  100 ASN cc_start: 0.7064 (m-40) cc_final: 0.6633 (m110)
REVERT: A  122 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6329 (mp)
REVERT: B    5 GLN cc_start: 0.5975 (OUTLIER) cc_final: 0.5452 (tt0)
REVERT: B   35 ASP cc_start: 0.6692 (m-30) cc_final: 0.6409 (m-30)
REVERT: B   57 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6846 (pm20)
REVERT: B   70 SER cc_start: 0.7467 (p) cc_final: 0.6849 (m)
REVERT: B  100 ASN cc_start: 0.7037 (m-40) cc_final: 0.6116 (t0)
REVERT: B  128 ARG cc_start: 0.7672 (ttp-170) cc_final: 0.7272 (ttp-170)
REVERT: B  129 PHE cc_start: 0.8008 (m-80) cc_final: 0.7506 (m-80)
REVERT: B  243 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7109 (mt-10)
REVERT: B  254 ARG cc_start: 0.6909 (ttm110) cc_final: 0.6611 (mtt-85)
REVERT: B  262 GLN cc_start: 0.7985 (pt0) cc_final: 0.7722 (pt0)
REVERT: B  299 PHE cc_start: 0.6296 (t80) cc_final: 0.5644 (t80)
REVERT: B  349 LYS cc_start: 0.6233 (mmtt) cc_final: 0.5999 (mmtm)
REVERT: C    9 GLU cc_start: 0.6769 (mt-10) cc_final: 0.5638 (mm-30)
REVERT: C   56 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6316 (mt0)
REVERT: C   89 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.6653 (mt0)
REVERT: C  100 ASN cc_start: 0.7057 (m-40) cc_final: 0.5776 (t0)
REVERT: C  201 LYS cc_start: 0.6950 (tppp) cc_final: 0.6667 (tmmt)
REVERT: C  254 ARG cc_start: 0.7308 (ttm-80) cc_final: 0.7022 (mtt-85)
REVERT: C  299 PHE cc_start: 0.5972 (t80) cc_final: 0.5448 (t80)
REVERT: C  345 TYR cc_start: 0.7301 (t80) cc_final: 0.6838 (t80)
REVERT: C  355 LYS cc_start: 0.6180 (mtpt) cc_final: 0.5093 (mmpt)
REVERT: D   89 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.6656 (mt0)
REVERT: D  100 ASN cc_start: 0.7167 (m-40) cc_final: 0.6090 (t0)
REVERT: D  222 ILE cc_start: 0.7240 (mt) cc_final: 0.6998 (mt)
REVERT: E   36 LYS cc_start: 0.6337 (ttmm) cc_final: 0.5588 (ttpt)
REVERT: E   56 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6407 (mt0)
REVERT: E  100 ASN cc_start: 0.7311 (m-40) cc_final: 0.6127 (t0)
REVERT: E  129 PHE cc_start: 0.8046 (m-80) cc_final: 0.7831 (m-80)
REVERT: E  139 LEU cc_start: 0.5974 (tp) cc_final: 0.5696 (tp)
REVERT: E  201 LYS cc_start: 0.6576 (tppp) cc_final: 0.6177 (tmmt)
REVERT: E  222 ILE cc_start: 0.6979 (mm) cc_final: 0.6741 (mt)
REVERT: E  262 GLN cc_start: 0.8009 (pt0) cc_final: 0.7796 (pt0)
REVERT: E  264 GLN cc_start: 0.8712 (tp40) cc_final: 0.8386 (tp40)
REVERT: F    5 GLN cc_start: 0.6060 (OUTLIER) cc_final: 0.5413 (tt0)
REVERT: F    9 GLU cc_start: 0.6248 (mt-10) cc_final: 0.5139 (mm-30)
REVERT: F   30 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7270 (mm)
REVERT: F   35 ASP cc_start: 0.6769 (m-30) cc_final: 0.6528 (m-30)
REVERT: F   36 LYS cc_start: 0.6483 (ttmt) cc_final: 0.6199 (ttmt)
REVERT: F   56 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6688 (mp10)
REVERT: F  100 ASN cc_start: 0.7385 (m-40) cc_final: 0.6138 (t0)
REVERT: F  122 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6352 (mp)
REVERT: F  299 PHE cc_start: 0.6290 (t80) cc_final: 0.5729 (t80)
REVERT: F  326 ASN cc_start: 0.6773 (OUTLIER) cc_final: 0.6106 (p0)
REVERT: F  343 LYS cc_start: 0.5469 (OUTLIER) cc_final: 0.4382 (mptp)
REVERT: G   70 SER cc_start: 0.7269 (p) cc_final: 0.6896 (m)
REVERT: G   89 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.5853 (mp10)
REVERT: G  100 ASN cc_start: 0.7371 (m110) cc_final: 0.6204 (t0)
REVERT: G  352 GLU cc_start: 0.6795 (tm-30) cc_final: 0.6573 (tp30)
  outliers start: 55
  outliers final: 26
  residues processed: 332
  average time/residue: 1.1875
  time to fit residues: 451.6929
Evaluate side-chains
  337 residues out of total 2177 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 295
  time to evaluate  : 2.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 ILE
Chi-restraints excluded: chain A residue    5 GLN
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain B residue    3 ILE
Chi-restraints excluded: chain B residue    5 GLN
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue  246 CYS
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue    5 GLN
Chi-restraints excluded: chain C residue   56 GLN
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain C residue   91 LYS
Chi-restraints excluded: chain C residue  246 CYS
Chi-restraints excluded: chain D residue    3 ILE
Chi-restraints excluded: chain D residue    5 GLN
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue   89 GLN
Chi-restraints excluded: chain D residue  214 ILE
Chi-restraints excluded: chain D residue  246 CYS
Chi-restraints excluded: chain E residue    5 GLN
Chi-restraints excluded: chain E residue   56 GLN
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  246 CYS
Chi-restraints excluded: chain E residue  258 THR
Chi-restraints excluded: chain F residue    3 ILE
Chi-restraints excluded: chain F residue    5 GLN
Chi-restraints excluded: chain F residue   30 LEU
Chi-restraints excluded: chain F residue   56 GLN
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain F residue  122 LEU
Chi-restraints excluded: chain F residue  222 ILE
Chi-restraints excluded: chain F residue  246 CYS
Chi-restraints excluded: chain F residue  326 ASN
Chi-restraints excluded: chain F residue  343 LYS
Chi-restraints excluded: chain G residue   89 GLN
Chi-restraints excluded: chain G residue  246 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 238
   random chunks:
   chunk 201 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 174 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 189 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 194 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 34 optimal weight:    6.9990
   chunk 166 optimal weight:    6.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  89 GLN
E 353 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.185267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.144993 restraints weight = 19087.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 1.27
r_work: 0.3346 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.4125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  20146  Z= 0.214
  Angle     :  0.568   8.516  27328  Z= 0.276
  Chirality :  0.039   0.139   3255
  Planarity :  0.004   0.039   3178
  Dihedral  : 11.441  63.818   4522
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 21.84 %
    Favored  : 75.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.18), residues: 2380
  helix:  2.07 (0.13), residues: 1561
  sheet: -0.14 (0.57), residues: 91
  loop : -1.46 (0.25), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP F  74 
 HIS   0.002   0.001   HIS F 106 
 PHE   0.022   0.002   PHE B 141 
 TYR   0.013   0.001   TYR D 230 
 ARG   0.007   0.001   ARG C 254 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7515.76 seconds
wall clock time: 136 minutes 21.56 seconds (8181.56 seconds total)