Starting phenix.real_space_refine
on Mon Apr 15 03:30:00 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v89_43031/04_2024/8v89_43031_trim_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v89_43031/04_2024/8v89_43031.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v89_43031/04_2024/8v89_43031.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v89_43031/04_2024/8v89_43031.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v89_43031/04_2024/8v89_43031_trim_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v89_43031/04_2024/8v89_43031_trim_updated.pdb"
  }
  resolution = 2.53
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.097
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: 6
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     S     115      5.16       5
     C   11030      2.51       5
     N    2615      2.21       5
     O    3105      1.98       5
     H   15855      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   70": "OE1" <-> "OE2"
    Residue "A ARG   78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A TYR  150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B GLU   70": "OE1" <-> "OE2"
    Residue "B ARG   78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B TYR  150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C GLU   70": "OE1" <-> "OE2"
    Residue "C ARG   78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "C TYR  150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D GLU   70": "OE1" <-> "OE2"
    Residue "D ARG   78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "D TYR  150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E GLU   70": "OE1" <-> "OE2"
    Residue "E ARG   78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "E TYR  150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib"
  Total number of atoms: 32725
  Number of models: 1
  Model: ""
    Number of chains: 25
    Chain: "A"
      Number of atoms: 6365
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 394, 6340
          Classifications: {'peptide': 394}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 394, 6341
          Classifications: {'peptide': 394}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 6400
    Chain: "B"
      Number of atoms: 6365
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 394, 6340
          Classifications: {'peptide': 394}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 394, 6341
          Classifications: {'peptide': 394}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 6400
    Chain: "C"
      Number of atoms: 6365
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 394, 6340
          Classifications: {'peptide': 394}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 394, 6341
          Classifications: {'peptide': 394}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 6400
    Chain: "D"
      Number of atoms: 6365
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 394, 6340
          Classifications: {'peptide': 394}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 394, 6341
          Classifications: {'peptide': 394}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 6400
    Chain: "E"
      Number of atoms: 6365
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 394, 6340
          Classifications: {'peptide': 394}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 394, 6341
          Classifications: {'peptide': 394}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 6400
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "I"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "J"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "K"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "L"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "M"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "N"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "O"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 110
          Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 1, 'R16': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'POV:plan-1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 110
          Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 1, 'R16': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'POV:plan-1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 110
          Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 1, 'R16': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'POV:plan-1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "D"
      Number of atoms: 110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 110
          Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 1, 'R16': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'POV:plan-1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "E"
      Number of atoms: 110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 110
          Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 1, 'R16': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'POV:plan-1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 14
          Classifications: {'water': 14}
          Link IDs: {None: 13}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 14
          Classifications: {'water': 14}
          Link IDs: {None: 13}
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 14
          Classifications: {'water': 14}
          Link IDs: {None: 13}
    Chain: "D"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 14
          Classifications: {'water': 14}
          Link IDs: {None: 13}
    Chain: "E"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 14
          Classifications: {'water': 14}
          Link IDs: {None: 13}
  Time building chain proxies: 26.92, per 1000 atoms: 0.82
  Number of scatterers: 32725
  At special positions: 0
  Unit cell: (98.175, 99, 164.175, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S     115     16.00
     P       5     15.00
     O    3105      8.00
     N    2615      7.00
     C   11030      6.00
     H   15855      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 127 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 189 " - pdb=" SG  CYS A 190 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 127 " - pdb=" SG  CYS B 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 189 " - pdb=" SG  CYS B 190 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 127 " - pdb=" SG  CYS C 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 189 " - pdb=" SG  CYS C 190 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 127 " - pdb=" SG  CYS D 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 189 " - pdb=" SG  CYS D 190 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 127 " - pdb=" SG  CYS E 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 189 " - pdb=" SG  CYS E 190 " distance=2.04

  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
    BETA1-4
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
      " NAG I   1 " - " NAG I   2 "
      " NAG J   1 " - " NAG J   2 "
      " NAG K   1 " - " NAG K   2 "
      " NAG L   1 " - " NAG L   2 "
      " NAG M   1 " - " NAG M   2 "
      " NAG N   1 " - " NAG N   2 "
      " NAG O   1 " - " NAG O   2 "
    NAG-ASN
      " NAG A 601 " - " ASN A  67 "
      " NAG B 602 " - " ASN B  67 "
      " NAG C 602 " - " ASN C  67 "
      " NAG D 602 " - " ASN D  67 "
      " NAG E 602 " - " ASN E  67 "
      " NAG F   1 " - " ASN A  23 "
      " NAG G   1 " - " ASN A 110 "
      " NAG H   1 " - " ASN B  23 "
      " NAG I   1 " - " ASN B 110 "
      " NAG J   1 " - " ASN C  23 "
      " NAG K   1 " - " ASN C 110 "
      " NAG L   1 " - " ASN D  23 "
      " NAG M   1 " - " ASN D 110 "
      " NAG N   1 " - " ASN E  23 "
      " NAG O   1 " - " ASN E 110 "
  Time building additional restraints: 27.51
  Conformation dependent library (CDL) restraints added in 6.4 seconds
  

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3780

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      45 helices and 25 sheets defined
      40.4% alpha, 19.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 4.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 11
    Processing helix  chain 'A' and resid 208 through 213
    Processing helix  chain 'A' and resid 215 through 230
      removed outlier: 3.859A  pdb=" N   LEU A 226 " --> pdb=" O   SER A 222 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   VAL A 228 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
      removed outlier: 4.807A  pdb=" N   PHE A 229 " --> pdb=" O   ALA A 225 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   LEU A 230 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 259
      removed outlier: 3.619A  pdb=" N   LEU A 254 " --> pdb=" O   THR A 250 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   LEU A 255 " --> pdb=" O   VAL A 251 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLU A 258 " --> pdb=" O   LEU A 254 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ILE A 259 " --> pdb=" O   LEU A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 295
    Processing helix  chain 'A' and resid 306 through 313
    Processing helix  chain 'A' and resid 315 through 319
    Processing helix  chain 'A' and resid 409 through 465
    Processing helix  chain 'A' and resid 470 through 477
    Processing helix  chain 'B' and resid 2 through 11
    Processing helix  chain 'B' and resid 208 through 213
    Processing helix  chain 'B' and resid 215 through 230
      removed outlier: 3.859A  pdb=" N   LEU B 226 " --> pdb=" O   SER B 222 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   VAL B 228 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
      removed outlier: 4.807A  pdb=" N   PHE B 229 " --> pdb=" O   ALA B 225 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   LEU B 230 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 259
      removed outlier: 3.619A  pdb=" N   LEU B 254 " --> pdb=" O   THR B 250 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   LEU B 255 " --> pdb=" O   VAL B 251 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLU B 258 " --> pdb=" O   LEU B 254 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ILE B 259 " --> pdb=" O   LEU B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 295
    Processing helix  chain 'B' and resid 306 through 313
    Processing helix  chain 'B' and resid 315 through 319
    Processing helix  chain 'B' and resid 409 through 465
    Processing helix  chain 'B' and resid 470 through 477
    Processing helix  chain 'C' and resid 2 through 11
    Processing helix  chain 'C' and resid 208 through 213
    Processing helix  chain 'C' and resid 215 through 230
      removed outlier: 3.859A  pdb=" N   LEU C 226 " --> pdb=" O   SER C 222 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   VAL C 228 " --> pdb=" O   LEU C 224 " (cutoff:3.500A)
      removed outlier: 4.808A  pdb=" N   PHE C 229 " --> pdb=" O   ALA C 225 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   LEU C 230 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 259
      removed outlier: 3.619A  pdb=" N   LEU C 254 " --> pdb=" O   THR C 250 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   LEU C 255 " --> pdb=" O   VAL C 251 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLU C 258 " --> pdb=" O   LEU C 254 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ILE C 259 " --> pdb=" O   LEU C 255 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 295
    Processing helix  chain 'C' and resid 306 through 313
    Processing helix  chain 'C' and resid 315 through 319
    Processing helix  chain 'C' and resid 409 through 465
    Processing helix  chain 'C' and resid 470 through 477
    Processing helix  chain 'D' and resid 2 through 11
    Processing helix  chain 'D' and resid 208 through 213
    Processing helix  chain 'D' and resid 215 through 230
      removed outlier: 3.860A  pdb=" N   LEU D 226 " --> pdb=" O   SER D 222 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   VAL D 228 " --> pdb=" O   LEU D 224 " (cutoff:3.500A)
      removed outlier: 4.807A  pdb=" N   PHE D 229 " --> pdb=" O   ALA D 225 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   LEU D 230 " --> pdb=" O   LEU D 226 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 238 through 259
      removed outlier: 3.619A  pdb=" N   LEU D 254 " --> pdb=" O   THR D 250 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   LEU D 255 " --> pdb=" O   VAL D 251 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLU D 258 " --> pdb=" O   LEU D 254 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ILE D 259 " --> pdb=" O   LEU D 255 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 295
    Processing helix  chain 'D' and resid 306 through 313
    Processing helix  chain 'D' and resid 315 through 319
    Processing helix  chain 'D' and resid 409 through 465
    Processing helix  chain 'D' and resid 470 through 477
    Processing helix  chain 'E' and resid 2 through 11
    Processing helix  chain 'E' and resid 208 through 213
    Processing helix  chain 'E' and resid 215 through 230
      removed outlier: 3.859A  pdb=" N   LEU E 226 " --> pdb=" O   SER E 222 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   VAL E 228 " --> pdb=" O   LEU E 224 " (cutoff:3.500A)
      removed outlier: 4.807A  pdb=" N   PHE E 229 " --> pdb=" O   ALA E 225 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   LEU E 230 " --> pdb=" O   LEU E 226 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 238 through 259
      removed outlier: 3.619A  pdb=" N   LEU E 254 " --> pdb=" O   THR E 250 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   LEU E 255 " --> pdb=" O   VAL E 251 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLU E 258 " --> pdb=" O   LEU E 254 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ILE E 259 " --> pdb=" O   LEU E 255 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 269 through 295
    Processing helix  chain 'E' and resid 306 through 313
    Processing helix  chain 'E' and resid 315 through 319
    Processing helix  chain 'E' and resid 409 through 465
    Processing helix  chain 'E' and resid 470 through 477
    Processing sheet with id=  A, first strand: chain 'A' and resid 155 through 159
      removed outlier: 6.105A  pdb=" N   LEU A  28 " --> pdb=" O   ASP A 156 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   GLN A 158 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   VAL A  30 " --> pdb=" O   GLN A 158 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ASN A  52 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 5.080A  pdb=" N   ILE A  39 " --> pdb=" O   THR A  50 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   THR A  50 " --> pdb=" O   ILE A  39 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 41 through 43
    Processing sheet with id=  C, first strand: chain 'A' and resid 57 through 60
    Processing sheet with id=  D, first strand: chain 'A' and resid 76 through 79
    Processing sheet with id=  E, first strand: chain 'A' and resid 89 through 91
      removed outlier: 3.527A  pdb=" N   GLY A 177 " --> pdb=" O   THR A 202 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   ARG A 204 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
      removed outlier: 5.485A  pdb=" N   LEU A 175 " --> pdb=" O   ARG A 204 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 155 through 159
      removed outlier: 6.105A  pdb=" N   LEU B  28 " --> pdb=" O   ASP B 156 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   GLN B 158 " --> pdb=" O   LEU B  28 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   VAL B  30 " --> pdb=" O   GLN B 158 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ASN B  52 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 5.081A  pdb=" N   ILE B  39 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   THR B  50 " --> pdb=" O   ILE B  39 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 41 through 43
    Processing sheet with id=  H, first strand: chain 'B' and resid 57 through 60
    Processing sheet with id=  I, first strand: chain 'B' and resid 76 through 79
    Processing sheet with id=  J, first strand: chain 'B' and resid 89 through 91
      removed outlier: 3.528A  pdb=" N   GLY B 177 " --> pdb=" O   THR B 202 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   ARG B 204 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
      removed outlier: 5.485A  pdb=" N   LEU B 175 " --> pdb=" O   ARG B 204 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'C' and resid 155 through 159
      removed outlier: 6.104A  pdb=" N   LEU C  28 " --> pdb=" O   ASP C 156 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   GLN C 158 " --> pdb=" O   LEU C  28 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   VAL C  30 " --> pdb=" O   GLN C 158 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ASN C  52 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 5.081A  pdb=" N   ILE C  39 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   THR C  50 " --> pdb=" O   ILE C  39 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'C' and resid 41 through 43
    Processing sheet with id=  M, first strand: chain 'C' and resid 57 through 60
    Processing sheet with id=  N, first strand: chain 'C' and resid 76 through 79
    Processing sheet with id=  O, first strand: chain 'C' and resid 89 through 91
      removed outlier: 3.527A  pdb=" N   GLY C 177 " --> pdb=" O   THR C 202 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   ARG C 204 " --> pdb=" O   LEU C 175 " (cutoff:3.500A)
      removed outlier: 5.486A  pdb=" N   LEU C 175 " --> pdb=" O   ARG C 204 " (cutoff:3.500A)
    Processing sheet with id=  P, first strand: chain 'D' and resid 155 through 159
      removed outlier: 6.105A  pdb=" N   LEU D  28 " --> pdb=" O   ASP D 156 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   GLN D 158 " --> pdb=" O   LEU D  28 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   VAL D  30 " --> pdb=" O   GLN D 158 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ASN D  52 " --> pdb=" O   LEU D  37 " (cutoff:3.500A)
      removed outlier: 5.080A  pdb=" N   ILE D  39 " --> pdb=" O   THR D  50 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   THR D  50 " --> pdb=" O   ILE D  39 " (cutoff:3.500A)
    Processing sheet with id=  Q, first strand: chain 'D' and resid 41 through 43
    Processing sheet with id=  R, first strand: chain 'D' and resid 57 through 60
    Processing sheet with id=  S, first strand: chain 'D' and resid 76 through 79
    Processing sheet with id=  T, first strand: chain 'D' and resid 89 through 91
      removed outlier: 3.527A  pdb=" N   GLY D 177 " --> pdb=" O   THR D 202 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   ARG D 204 " --> pdb=" O   LEU D 175 " (cutoff:3.500A)
      removed outlier: 5.485A  pdb=" N   LEU D 175 " --> pdb=" O   ARG D 204 " (cutoff:3.500A)
    Processing sheet with id=  U, first strand: chain 'E' and resid 155 through 159
      removed outlier: 6.105A  pdb=" N   LEU E  28 " --> pdb=" O   ASP E 156 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   GLN E 158 " --> pdb=" O   LEU E  28 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   VAL E  30 " --> pdb=" O   GLN E 158 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ASN E  52 " --> pdb=" O   LEU E  37 " (cutoff:3.500A)
      removed outlier: 5.081A  pdb=" N   ILE E  39 " --> pdb=" O   THR E  50 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   THR E  50 " --> pdb=" O   ILE E  39 " (cutoff:3.500A)
    Processing sheet with id=  V, first strand: chain 'E' and resid 41 through 43
    Processing sheet with id=  W, first strand: chain 'E' and resid 57 through 60
    Processing sheet with id=  X, first strand: chain 'E' and resid 76 through 79
    Processing sheet with id=  Y, first strand: chain 'E' and resid 89 through 91
      removed outlier: 3.528A  pdb=" N   GLY E 177 " --> pdb=" O   THR E 202 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   ARG E 204 " --> pdb=" O   LEU E 175 " (cutoff:3.500A)
      removed outlier: 5.486A  pdb=" N   LEU E 175 " --> pdb=" O   ARG E 204 " (cutoff:3.500A)

    780 hydrogen bonds defined for protein.
    2260 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: 12.15

  Time building geometry restraints manager: 28.66 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 15820
        1.04 -     1.24: 2110
        1.24 -     1.44: 5321
        1.44 -     1.64: 9709
        1.64 -     1.84: 170
  Bond restraints: 33130
  Sorted by residual:
  bond pdb=" NZ  LYS B 303 "
       pdb=" HZ3 LYS B 303 "
    ideal  model  delta    sigma   weight residual
    0.890  0.971 -0.081 2.00e-02 2.50e+03 1.65e+01
  bond pdb=" NZ  LYS D 412 "
       pdb=" HZ2 LYS D 412 "
    ideal  model  delta    sigma   weight residual
    0.890  0.971 -0.081 2.00e-02 2.50e+03 1.65e+01
  bond pdb=" NZ  LYS E  45 "
       pdb=" HZ3 LYS E  45 "
    ideal  model  delta    sigma   weight residual
    0.890  0.971 -0.081 2.00e-02 2.50e+03 1.64e+01
  bond pdb=" NZ  LYS B   5 "
       pdb=" HZ3 LYS B   5 "
    ideal  model  delta    sigma   weight residual
    0.890  0.971 -0.081 2.00e-02 2.50e+03 1.64e+01
  bond pdb=" NZ  LYS C   5 "
       pdb=" HZ1 LYS C   5 "
    ideal  model  delta    sigma   weight residual
    0.890  0.971 -0.081 2.00e-02 2.50e+03 1.64e+01
  ... (remaining 33125 not shown)

  Histogram of bond angle deviations from ideal:
       97.58 -   104.89: 527
      104.89 -   112.19: 37269
      112.19 -   119.50: 8520
      119.50 -   126.80: 12913
      126.80 -   134.11: 331
  Bond angle restraints: 59560
  Sorted by residual:
  angle pdb=" N   ASN D 110 "
        pdb=" CA  ASN D 110 "
        pdb=" CB  ASN D 110 "
      ideal   model   delta    sigma   weight residual
     110.51  117.28   -6.77 1.61e+00 3.86e-01 1.77e+01
  angle pdb=" N   ASN A 110 "
        pdb=" CA  ASN A 110 "
        pdb=" CB  ASN A 110 "
      ideal   model   delta    sigma   weight residual
     110.51  117.28   -6.77 1.61e+00 3.86e-01 1.77e+01
  angle pdb=" N   ASN C 110 "
        pdb=" CA  ASN C 110 "
        pdb=" CB  ASN C 110 "
      ideal   model   delta    sigma   weight residual
     110.51  117.26   -6.75 1.61e+00 3.86e-01 1.76e+01
  angle pdb=" N   ASN B 110 "
        pdb=" CA  ASN B 110 "
        pdb=" CB  ASN B 110 "
      ideal   model   delta    sigma   weight residual
     110.51  117.26   -6.75 1.61e+00 3.86e-01 1.76e+01
  angle pdb=" N   ASN E 110 "
        pdb=" CA  ASN E 110 "
        pdb=" CB  ASN E 110 "
      ideal   model   delta    sigma   weight residual
     110.51  117.26   -6.75 1.61e+00 3.86e-01 1.76e+01
  ... (remaining 59555 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.04: 15705
       25.04 -    50.08: 635
       50.08 -    75.13: 150
       75.13 -   100.17: 35
      100.17 -   125.21: 15
  Dihedral angle restraints: 16540
    sinusoidal: 9345
      harmonic: 7195
  Sorted by residual:
  dihedral pdb=" CA  CYS B 189 "
           pdb=" C   CYS B 189 "
           pdb=" N   CYS B 190 "
           pdb=" CA  CYS B 190 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.46  -25.54     0      5.00e+00 4.00e-02 2.61e+01
  dihedral pdb=" CA  CYS C 189 "
           pdb=" C   CYS C 189 "
           pdb=" N   CYS C 190 "
           pdb=" CA  CYS C 190 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.49  -25.51     0      5.00e+00 4.00e-02 2.60e+01
  dihedral pdb=" CA  CYS A 189 "
           pdb=" C   CYS A 189 "
           pdb=" N   CYS A 190 "
           pdb=" CA  CYS A 190 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.50  -25.50     0      5.00e+00 4.00e-02 2.60e+01
  ... (remaining 16537 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.101: 2529
       0.101 -    0.203: 156
       0.203 -    0.304: 5
       0.304 -    0.405: 0
       0.405 -    0.506: 5
  Chirality restraints: 2695
  Sorted by residual:
  chirality pdb=" C1  NAG J   2 "
            pdb=" O4  NAG J   1 "
            pdb=" C2  NAG J   2 "
            pdb=" O5  NAG J   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.30   -0.10 2.00e-02 2.50e+03 2.51e+01
  chirality pdb=" C1  NAG N   2 "
            pdb=" O4  NAG N   1 "
            pdb=" C2  NAG N   2 "
            pdb=" O5  NAG N   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.30   -0.10 2.00e-02 2.50e+03 2.42e+01
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.30   -0.10 2.00e-02 2.50e+03 2.40e+01
  ... (remaining 2692 not shown)

  Planarity restraints: 4700
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG L   2 "   -0.316 2.00e-02 2.50e+03   2.73e-01 9.32e+02
        pdb=" C7  NAG L   2 "    0.074 2.00e-02 2.50e+03
        pdb=" C8  NAG L   2 "   -0.031 2.00e-02 2.50e+03
        pdb=" N2  NAG L   2 "    0.475 2.00e-02 2.50e+03
        pdb=" O7  NAG L   2 "   -0.202 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F   2 "    0.315 2.00e-02 2.50e+03   2.73e-01 9.32e+02
        pdb=" C7  NAG F   2 "   -0.073 2.00e-02 2.50e+03
        pdb=" C8  NAG F   2 "    0.031 2.00e-02 2.50e+03
        pdb=" N2  NAG F   2 "   -0.475 2.00e-02 2.50e+03
        pdb=" O7  NAG F   2 "    0.202 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG H   2 "    0.315 2.00e-02 2.50e+03   2.73e-01 9.31e+02
        pdb=" C7  NAG H   2 "   -0.074 2.00e-02 2.50e+03
        pdb=" C8  NAG H   2 "    0.031 2.00e-02 2.50e+03
        pdb=" N2  NAG H   2 "   -0.475 2.00e-02 2.50e+03
        pdb=" O7  NAG H   2 "    0.202 2.00e-02 2.50e+03
  ... (remaining 4697 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 1858
        2.20 -     2.80: 65428
        2.80 -     3.40: 91344
        3.40 -     4.00: 125115
        4.00 -     4.60: 187725
  Nonbonded interactions: 471470
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP D  81 "
            pdb=" HD1 HIS D 104 "
     model   vdw
     1.604 1.850
  nonbonded pdb=" OD2 ASP A  81 "
            pdb=" HD1 HIS A 104 "
     model   vdw
     1.604 1.850
  nonbonded pdb=" OD2 ASP E  81 "
            pdb=" HD1 HIS E 104 "
     model   vdw
     1.604 1.850
  nonbonded pdb=" OD2 ASP C  81 "
            pdb=" HD1 HIS C 104 "
     model   vdw
     1.604 1.850
  nonbonded pdb=" OD2 ASP B  81 "
            pdb=" HD1 HIS B 104 "
     model   vdw
     1.604 1.850
  ... (remaining 471465 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 55 or resid 57 through 113 or resid 115 through  \ 
478))
  selection = (chain 'B' and (resid 1 through 55 or resid 57 through 113 or resid 115 through  \ 
478))
  selection = (chain 'C' and (resid 1 through 55 or resid 57 through 113 or resid 115 through  \ 
478))
  selection = (chain 'D' and (resid 1 through 55 or resid 57 through 113 or resid 115 through  \ 
478))
  selection = (chain 'E' and (resid 1 through 55 or resid 57 through 113 or resid 115 through  \ 
478))
}
ncs_group {
  reference = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=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:             2.420
  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:             0.510
  Extract box with map and model:          9.710
  Check model and map are aligned:         0.510
  Set scattering table:                    0.350
  Process input model:                     121.040
  Find NCS groups from input model:        1.790
  Set up NCS constraints:                  0.260
  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:12.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  148.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
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      :  0.008   0.080  17270  Z= 0.507
  Angle     :  0.983   6.870  23510  Z= 0.533
  Chirality :  0.056   0.506   2695
  Planarity :  0.014   0.273   2825
  Dihedral  : 15.417 125.211   7155
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  1.68 %
    Favored  : 97.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -1.75 (0.16), residues: 1960
  helix: -1.22 (0.15), residues: 790
  sheet: -1.05 (0.21), residues: 440
  loop : -0.86 (0.22), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D 437 
 HIS   0.006   0.002   HIS B 296 
 PHE   0.020   0.003   PHE E 186 
 TYR   0.017   0.004   TYR B 194 
 ARG   0.009   0.001   ARG C 206 

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

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

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  387 residues out of total 1770 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 377
  time to evaluate  : 2.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8474 (mpt90)
REVERT: B   18 GLU cc_start: 0.8062 (tt0) cc_final: 0.7857 (tt0)
REVERT: B  274 PHE cc_start: 0.7351 (m-10) cc_final: 0.7067 (m-10)
REVERT: C  249 LEU cc_start: 0.8504 (tp) cc_final: 0.8242 (tm)
REVERT: D  160 GLN cc_start: 0.8259 (mt0) cc_final: 0.8046 (mt0)
REVERT: D  186 PHE cc_start: 0.7588 (m-80) cc_final: 0.7340 (m-80)
REVERT: D  238 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8739 (mtpp)
REVERT: E   92 TYR cc_start: 0.8519 (m-10) cc_final: 0.8282 (m-10)
REVERT: E  455 PHE cc_start: 0.7557 (t80) cc_final: 0.7146 (t80)
  outliers start: 10
  outliers final: 1
  residues processed: 387
  average time/residue: 2.1933
  time to fit residues: 970.1482
Evaluate side-chains
  336 residues out of total 1770 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 333
  time to evaluate  : 2.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain B residue   78 ARG
Chi-restraints excluded: chain D residue  238 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 164 optimal weight:    1.9990
   chunk 147 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 99 optimal weight:    0.8980
   chunk 78 optimal weight:    0.6980
   chunk 152 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 177 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  47 GLN
B 160 GLN
B 293 GLN
C  47 GLN
C 293 GLN
D  26 GLN
D  47 GLN
E  26 GLN
E  47 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.1331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  17270  Z= 0.208
  Angle     :  0.621   5.749  23510  Z= 0.321
  Chirality :  0.042   0.160   2695
  Planarity :  0.004   0.061   2825
  Dihedral  : 12.214 120.027   3387
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  :  8.72 %
    Favored  : 89.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.08 (0.18), residues: 1960
  helix:  0.86 (0.16), residues: 810
  sheet: -0.51 (0.22), residues: 440
  loop : -0.32 (0.23), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 437 
 HIS   0.003   0.001   HIS B 104 
 PHE   0.021   0.002   PHE A  99 
 TYR   0.011   0.002   TYR A 117 
 ARG   0.008   0.001   ARG E 446 

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

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

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  389 residues out of total 1770 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 357
  time to evaluate  : 2.662 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  216 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7514 (mp)
REVERT: A  417 VAL cc_start: 0.7488 (t) cc_final: 0.7280 (t)
REVERT: B  216 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7451 (mp)
REVERT: B  298 ASP cc_start: 0.7856 (t0) cc_final: 0.7573 (t0)
REVERT: B  450 MET cc_start: 0.5947 (mmm) cc_final: 0.5594 (mmm)
REVERT: C   18 GLU cc_start: 0.8079 (tt0) cc_final: 0.7736 (tt0)
REVERT: C  472 GLU cc_start: 0.7420 (tt0) cc_final: 0.7110 (tt0)
REVERT: D  186 PHE cc_start: 0.7398 (m-80) cc_final: 0.7194 (m-80)
REVERT: D  446 ARG cc_start: 0.7814 (tpp80) cc_final: 0.7580 (tpp80)
REVERT: E  216 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7352 (mp)
REVERT: E  455 PHE cc_start: 0.7497 (t80) cc_final: 0.7128 (t80)
  outliers start: 32
  outliers final: 17
  residues processed: 374
  average time/residue: 2.0968
  time to fit residues: 908.8616
Evaluate side-chains
  361 residues out of total 1770 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 341
  time to evaluate  : 2.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain B residue   78 ARG
Chi-restraints excluded: chain B residue  216 ILE
Chi-restraints excluded: chain B residue  222 SER
Chi-restraints excluded: chain B residue  238 LYS
Chi-restraints excluded: chain C residue  290 ILE
Chi-restraints excluded: chain C residue  475 SER
Chi-restraints excluded: chain D residue   78 ARG
Chi-restraints excluded: chain D residue  221 ILE
Chi-restraints excluded: chain D residue  290 ILE
Chi-restraints excluded: chain D residue  475 SER
Chi-restraints excluded: chain E residue   78 ARG
Chi-restraints excluded: chain E residue  216 ILE
Chi-restraints excluded: chain E residue  222 SER
Chi-restraints excluded: chain E residue  238 LYS
Chi-restraints excluded: chain E residue  290 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 147 optimal weight:    0.9980
   chunk 120 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 177 optimal weight:    1.9990
   chunk 191 optimal weight:    2.9990
   chunk 157 optimal weight:    2.9990
   chunk 175 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 142 optimal weight:    2.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN    A
A 158 GLN
** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 158 GLN
D  47 GLN
D 158 GLN
E  47 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  17270  Z= 0.392
  Angle     :  0.721  11.324  23510  Z= 0.372
  Chirality :  0.044   0.252   2695
  Planarity :  0.006   0.066   2825
  Dihedral  : 11.975 111.769   3383
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  :  8.44 %
    Favored  : 88.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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:  0.16 (0.18), residues: 1960
  helix:  0.83 (0.16), residues: 855
  sheet: -0.50 (0.22), residues: 435
  loop : -0.19 (0.24), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 148 
 HIS   0.004   0.001   HIS B  62 
 PHE   0.017   0.003   PHE B  99 
 TYR   0.018   0.003   TYR A 419 
 ARG   0.006   0.001   ARG B   4 

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

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

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  380 residues out of total 1770 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 332
  time to evaluate  : 2.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ASN cc_start: 0.6732 (t0) cc_final: 0.6369 (m110)
REVERT: A   78 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8498 (mpt90)
REVERT: A  174 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.7106 (t0)
REVERT: A  216 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7726 (mp)
REVERT: A  278 MET cc_start: 0.6595 (OUTLIER) cc_final: 0.6015 (mpt)
REVERT: B   41 ASP cc_start: 0.7702 (t0) cc_final: 0.7388 (t0)
REVERT: B  450 MET cc_start: 0.5992 (mmm) cc_final: 0.5611 (mmm)
REVERT: B  472 GLU cc_start: 0.7498 (tt0) cc_final: 0.7131 (tt0)
REVERT: C  450 MET cc_start: 0.7002 (ptm) cc_final: 0.6734 (ptm)
REVERT: C  472 GLU cc_start: 0.7566 (tt0) cc_final: 0.7123 (tt0)
REVERT: D   78 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8690 (pmm150)
REVERT: D  216 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7731 (mp)
REVERT: D  446 ARG cc_start: 0.7865 (tpp80) cc_final: 0.7628 (tpp80)
REVERT: E   92 TYR cc_start: 0.8542 (m-10) cc_final: 0.8252 (m-10)
REVERT: E  216 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7533 (mp)
REVERT: E  252 PHE cc_start: 0.8302 (t80) cc_final: 0.8096 (t80)
REVERT: E  278 MET cc_start: 0.6598 (OUTLIER) cc_final: 0.5551 (mpt)
REVERT: E  455 PHE cc_start: 0.7567 (t80) cc_final: 0.7169 (t80)
  outliers start: 48
  outliers final: 22
  residues processed: 350
  average time/residue: 2.0686
  time to fit residues: 834.3452
Evaluate side-chains
  358 residues out of total 1770 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 328
  time to evaluate  : 2.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  174 ASP
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  222 SER
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  278 MET
Chi-restraints excluded: chain A residue  416 GLU
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain B residue   78 ARG
Chi-restraints excluded: chain B residue  216 ILE
Chi-restraints excluded: chain B residue  222 SER
Chi-restraints excluded: chain B residue  238 LYS
Chi-restraints excluded: chain C residue  238 LYS
Chi-restraints excluded: chain C residue  290 ILE
Chi-restraints excluded: chain C residue  475 SER
Chi-restraints excluded: chain D residue   69 SER
Chi-restraints excluded: chain D residue   78 ARG
Chi-restraints excluded: chain D residue  216 ILE
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  290 ILE
Chi-restraints excluded: chain D residue  431 GLU
Chi-restraints excluded: chain D residue  475 SER
Chi-restraints excluded: chain E residue   69 SER
Chi-restraints excluded: chain E residue  216 ILE
Chi-restraints excluded: chain E residue  222 SER
Chi-restraints excluded: chain E residue  238 LYS
Chi-restraints excluded: chain E residue  278 MET
Chi-restraints excluded: chain E residue  290 ILE
Chi-restraints excluded: chain E residue  416 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 175 optimal weight:    2.9990
   chunk 133 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   chunk 119 optimal weight:    2.9990
   chunk 178 optimal weight:    3.9990
   chunk 188 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 168 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 GLN
D  47 GLN
D 106 ASN
E  26 GLN
E  47 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  17270  Z= 0.249
  Angle     :  0.597   7.973  23510  Z= 0.308
  Chirality :  0.040   0.140   2695
  Planarity :  0.005   0.050   2825
  Dihedral  : 11.056 106.013   3383
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  :  9.72 %
    Favored  : 87.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.60 (0.18), residues: 1960
  helix:  1.40 (0.17), residues: 825
  sheet: -0.48 (0.23), residues: 430
  loop : -0.08 (0.23), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 133 
 HIS   0.002   0.001   HIS B 297 
 PHE   0.015   0.002   PHE C 470 
 TYR   0.011   0.002   TYR A 419 
 ARG   0.006   0.001   ARG E 446 

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

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

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  375 residues out of total 1770 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 333
  time to evaluate  : 2.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ASN cc_start: 0.6615 (t0) cc_final: 0.6186 (m-40)
REVERT: A   78 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8449 (mpt90)
REVERT: A  278 MET cc_start: 0.6541 (OUTLIER) cc_final: 0.6043 (mpt)
REVERT: A  417 VAL cc_start: 0.7478 (t) cc_final: 0.7268 (t)
REVERT: B   41 ASP cc_start: 0.7642 (t0) cc_final: 0.7269 (t0)
REVERT: B   44 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.5742 (mm-30)
REVERT: B  278 MET cc_start: 0.6531 (OUTLIER) cc_final: 0.5650 (mpt)
REVERT: B  450 MET cc_start: 0.5946 (mmm) cc_final: 0.5565 (mmm)
REVERT: B  472 GLU cc_start: 0.7463 (tt0) cc_final: 0.7092 (tt0)
REVERT: C  294 TYR cc_start: 0.8662 (m-80) cc_final: 0.8388 (m-80)
REVERT: C  472 GLU cc_start: 0.7468 (tt0) cc_final: 0.7070 (tt0)
REVERT: D   78 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8722 (pmm150)
REVERT: D  274 PHE cc_start: 0.6994 (m-10) cc_final: 0.6004 (m-10)
REVERT: D  278 MET cc_start: 0.6509 (OUTLIER) cc_final: 0.5580 (mpt)
REVERT: D  294 TYR cc_start: 0.8637 (m-80) cc_final: 0.8309 (m-80)
REVERT: D  446 ARG cc_start: 0.7838 (tpp80) cc_final: 0.7589 (tpp80)
REVERT: E  216 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7502 (mp)
REVERT: E  278 MET cc_start: 0.6463 (OUTLIER) cc_final: 0.5487 (mpt)
REVERT: E  455 PHE cc_start: 0.7536 (t80) cc_final: 0.7124 (t80)
  outliers start: 42
  outliers final: 21
  residues processed: 351
  average time/residue: 2.1267
  time to fit residues: 858.3576
Evaluate side-chains
  358 residues out of total 1770 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 329
  time to evaluate  : 4.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  222 SER
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  278 MET
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain B residue   44 GLU
Chi-restraints excluded: chain B residue   67 ASN
Chi-restraints excluded: chain B residue   78 ARG
Chi-restraints excluded: chain B residue  216 ILE
Chi-restraints excluded: chain B residue  222 SER
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  278 MET
Chi-restraints excluded: chain C residue  238 LYS
Chi-restraints excluded: chain C residue  290 ILE
Chi-restraints excluded: chain C residue  475 SER
Chi-restraints excluded: chain D residue   78 ARG
Chi-restraints excluded: chain D residue  222 SER
Chi-restraints excluded: chain D residue  238 LYS
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  278 MET
Chi-restraints excluded: chain D residue  290 ILE
Chi-restraints excluded: chain D residue  431 GLU
Chi-restraints excluded: chain D residue  475 SER
Chi-restraints excluded: chain E residue   69 SER
Chi-restraints excluded: chain E residue  216 ILE
Chi-restraints excluded: chain E residue  222 SER
Chi-restraints excluded: chain E residue  278 MET
Chi-restraints excluded: chain E residue  290 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 156 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 140 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 160 optimal weight:    3.9990
   chunk 130 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 169 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 293 GLN
B  47 GLN
C  47 GLN
D  47 GLN
E  26 GLN
E  47 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  17270  Z= 0.261
  Angle     :  0.593   5.624  23510  Z= 0.306
  Chirality :  0.040   0.164   2695
  Planarity :  0.005   0.055   2825
  Dihedral  : 10.609  97.211   3383
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 10.28 %
    Favored  : 87.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.18), residues: 1960
  helix:  1.57 (0.17), residues: 830
  sheet: -0.41 (0.23), residues: 430
  loop :  0.02 (0.24), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 133 
 HIS   0.002   0.001   HIS B  62 
 PHE   0.015   0.002   PHE C 470 
 TYR   0.012   0.002   TYR A 419 
 ARG   0.007   0.001   ARG E 446 

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

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

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  379 residues out of total 1770 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 340
  time to evaluate  : 2.657 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ASN cc_start: 0.6736 (t0) cc_final: 0.6279 (m-40)
REVERT: A   78 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8157 (mpt-90)
REVERT: A  278 MET cc_start: 0.6547 (OUTLIER) cc_final: 0.6087 (mpt)
REVERT: A  417 VAL cc_start: 0.7440 (t) cc_final: 0.7222 (t)
REVERT: B   41 ASP cc_start: 0.7686 (t0) cc_final: 0.7347 (t0)
REVERT: B   44 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.5689 (mm-30)
REVERT: B  278 MET cc_start: 0.6483 (OUTLIER) cc_final: 0.5594 (mpt)
REVERT: B  294 TYR cc_start: 0.8622 (m-80) cc_final: 0.8365 (m-80)
REVERT: B  450 MET cc_start: 0.5958 (mmm) cc_final: 0.5555 (mmm)
REVERT: B  472 GLU cc_start: 0.7477 (tt0) cc_final: 0.7130 (tt0)
REVERT: C  128 TYR cc_start: 0.7332 (t80) cc_final: 0.7029 (t80)
REVERT: C  294 TYR cc_start: 0.8664 (m-80) cc_final: 0.8412 (m-80)
REVERT: C  472 GLU cc_start: 0.7457 (tt0) cc_final: 0.7047 (tt0)
REVERT: D   78 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8557 (pmm150)
REVERT: D  274 PHE cc_start: 0.6997 (m-10) cc_final: 0.5971 (m-10)
REVERT: D  278 MET cc_start: 0.6469 (OUTLIER) cc_final: 0.5496 (mpt)
REVERT: D  294 TYR cc_start: 0.8618 (m-80) cc_final: 0.8318 (m-80)
REVERT: D  446 ARG cc_start: 0.7839 (tpp80) cc_final: 0.7595 (tpp80)
REVERT: E  216 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7543 (mp)
REVERT: E  278 MET cc_start: 0.6460 (OUTLIER) cc_final: 0.5544 (mpt)
REVERT: E  455 PHE cc_start: 0.7539 (t80) cc_final: 0.7173 (t80)
REVERT: E  472 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7232 (tt0)
  outliers start: 39
  outliers final: 23
  residues processed: 358
  average time/residue: 2.0980
  time to fit residues: 863.5148
Evaluate side-chains
  361 residues out of total 1770 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 329
  time to evaluate  : 2.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  222 SER
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  278 MET
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain B residue   44 GLU
Chi-restraints excluded: chain B residue   67 ASN
Chi-restraints excluded: chain B residue   69 SER
Chi-restraints excluded: chain B residue   78 ARG
Chi-restraints excluded: chain B residue  216 ILE
Chi-restraints excluded: chain B residue  222 SER
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  278 MET
Chi-restraints excluded: chain C residue  238 LYS
Chi-restraints excluded: chain C residue  290 ILE
Chi-restraints excluded: chain C residue  475 SER
Chi-restraints excluded: chain D residue   78 ARG
Chi-restraints excluded: chain D residue  222 SER
Chi-restraints excluded: chain D residue  238 LYS
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  278 MET
Chi-restraints excluded: chain D residue  290 ILE
Chi-restraints excluded: chain D residue  431 GLU
Chi-restraints excluded: chain D residue  475 SER
Chi-restraints excluded: chain E residue   69 SER
Chi-restraints excluded: chain E residue  216 ILE
Chi-restraints excluded: chain E residue  222 SER
Chi-restraints excluded: chain E residue  278 MET
Chi-restraints excluded: chain E residue  290 ILE
Chi-restraints excluded: chain E residue  416 GLU
Chi-restraints excluded: chain E residue  472 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 169 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 110 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 188 optimal weight:    4.9990
   chunk 156 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
B  47 GLN
D  26 GLN
D  47 GLN
E  26 GLN
E  47 GLN
E  56 GLN    A
** E 114 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
E 158 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  17270  Z= 0.326
  Angle     :  0.636   6.015  23510  Z= 0.330
  Chirality :  0.042   0.239   2695
  Planarity :  0.005   0.059   2825
  Dihedral  : 10.539  87.895   3383
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  :  9.94 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.72 (0.18), residues: 1960
  helix:  1.52 (0.17), residues: 825
  sheet: -0.39 (0.23), residues: 435
  loop : -0.05 (0.24), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 133 
 HIS   0.003   0.001   HIS B 297 
 PHE   0.016   0.002   PHE C 470 
 TYR   0.014   0.002   TYR A  31 
 ARG   0.008   0.001   ARG C 446 

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

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

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  372 residues out of total 1770 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 328
  time to evaluate  : 2.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ASN cc_start: 0.6805 (t0) cc_final: 0.6371 (m-40)
REVERT: A   69 SER cc_start: 0.7365 (m) cc_final: 0.7072 (t)
REVERT: A   78 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8172 (mpt-90)
REVERT: A  216 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7819 (mp)
REVERT: A  417 VAL cc_start: 0.7490 (t) cc_final: 0.7249 (t)
REVERT: B   41 ASP cc_start: 0.7675 (t0) cc_final: 0.7339 (t0)
REVERT: B  216 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7672 (mp)
REVERT: B  294 TYR cc_start: 0.8637 (m-80) cc_final: 0.8306 (m-80)
REVERT: B  450 MET cc_start: 0.5986 (mmm) cc_final: 0.5557 (mmm)
REVERT: B  472 GLU cc_start: 0.7494 (tt0) cc_final: 0.7097 (tt0)
REVERT: C  128 TYR cc_start: 0.7361 (t80) cc_final: 0.7046 (t80)
REVERT: C  294 TYR cc_start: 0.8700 (m-80) cc_final: 0.8366 (m-80)
REVERT: C  472 GLU cc_start: 0.7520 (tt0) cc_final: 0.7082 (tt0)
REVERT: D  294 TYR cc_start: 0.8651 (m-80) cc_final: 0.8307 (m-80)
REVERT: D  446 ARG cc_start: 0.7855 (tpp80) cc_final: 0.7616 (tpp80)
REVERT: E   92 TYR cc_start: 0.8493 (m-10) cc_final: 0.8271 (m-10)
REVERT: E  181 LYS cc_start: 0.7934 (tttt) cc_final: 0.7643 (tmtt)
REVERT: E  216 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7622 (mp)
REVERT: E  278 MET cc_start: 0.6361 (OUTLIER) cc_final: 0.5515 (mpt)
REVERT: E  455 PHE cc_start: 0.7557 (t80) cc_final: 0.7180 (t80)
REVERT: E  472 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7254 (tt0)
  outliers start: 44
  outliers final: 24
  residues processed: 343
  average time/residue: 2.0660
  time to fit residues: 817.9256
Evaluate side-chains
  360 residues out of total 1770 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 330
  time to evaluate  : 2.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  222 SER
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain B residue   67 ASN
Chi-restraints excluded: chain B residue   69 SER
Chi-restraints excluded: chain B residue   78 ARG
Chi-restraints excluded: chain B residue  216 ILE
Chi-restraints excluded: chain B residue  222 SER
Chi-restraints excluded: chain B residue  238 LYS
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain C residue  238 LYS
Chi-restraints excluded: chain C residue  290 ILE
Chi-restraints excluded: chain C residue  475 SER
Chi-restraints excluded: chain D residue  222 SER
Chi-restraints excluded: chain D residue  238 LYS
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  290 ILE
Chi-restraints excluded: chain D residue  431 GLU
Chi-restraints excluded: chain D residue  475 SER
Chi-restraints excluded: chain E residue   69 SER
Chi-restraints excluded: chain E residue  216 ILE
Chi-restraints excluded: chain E residue  221 ILE
Chi-restraints excluded: chain E residue  222 SER
Chi-restraints excluded: chain E residue  278 MET
Chi-restraints excluded: chain E residue  290 ILE
Chi-restraints excluded: chain E residue  416 GLU
Chi-restraints excluded: chain E residue  472 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 181 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 107 optimal weight:    0.0370
   chunk 137 optimal weight:    2.9990
   chunk 106 optimal weight:    0.6980
   chunk 158 optimal weight:    0.0040
   chunk 105 optimal weight:    1.9990
   chunk 187 optimal weight:    0.7980
   chunk 117 optimal weight:    1.9990
   chunk 114 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.4870

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

Flipped N/Q/H residues before XYZ refinement:
B  47 GLN
B 427 GLN
C  47 GLN
D  47 GLN
E  26 GLN
E  47 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  17270  Z= 0.156
  Angle     :  0.523   5.619  23510  Z= 0.269
  Chirality :  0.040   0.290   2695
  Planarity :  0.004   0.055   2825
  Dihedral  :  9.947  79.528   3383
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.17 %
    Favored  : 87.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.23 (0.19), residues: 1960
  helix:  1.92 (0.17), residues: 830
  sheet: -0.14 (0.23), residues: 430
  loop :  0.25 (0.24), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 133 
 HIS   0.002   0.000   HIS B 104 
 PHE   0.012   0.001   PHE E 470 
 TYR   0.007   0.001   TYR D 194 
 ARG   0.009   0.000   ARG A 446 

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

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

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  361 residues out of total 1770 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 335
  time to evaluate  : 2.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ASN cc_start: 0.6749 (t0) cc_final: 0.6369 (m-40)
REVERT: A   69 SER cc_start: 0.7328 (m) cc_final: 0.7039 (t)
REVERT: A   78 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8227 (mpt-90)
REVERT: A  212 LEU cc_start: 0.8056 (mt) cc_final: 0.7610 (mm)
REVERT: B   70 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6988 (mt-10)
REVERT: B  450 MET cc_start: 0.5898 (mmm) cc_final: 0.5460 (mmm)
REVERT: C  294 TYR cc_start: 0.8672 (m-80) cc_final: 0.8462 (m-80)
REVERT: C  455 PHE cc_start: 0.7472 (t80) cc_final: 0.7263 (t80)
REVERT: C  472 GLU cc_start: 0.7363 (tt0) cc_final: 0.7083 (tt0)
REVERT: D   97 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6744 (mp0)
REVERT: D  294 TYR cc_start: 0.8595 (m-80) cc_final: 0.8379 (m-80)
REVERT: D  446 ARG cc_start: 0.7811 (tpp80) cc_final: 0.7580 (tpp80)
REVERT: E  216 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7525 (mm)
REVERT: E  455 PHE cc_start: 0.7492 (t80) cc_final: 0.7148 (t80)
  outliers start: 26
  outliers final: 15
  residues processed: 345
  average time/residue: 2.1627
  time to fit residues: 857.9372
Evaluate side-chains
  343 residues out of total 1770 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 325
  time to evaluate  : 2.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain B residue   78 ARG
Chi-restraints excluded: chain B residue  216 ILE
Chi-restraints excluded: chain B residue  222 SER
Chi-restraints excluded: chain B residue  238 LYS
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain C residue  290 ILE
Chi-restraints excluded: chain C residue  475 SER
Chi-restraints excluded: chain D residue   97 GLU
Chi-restraints excluded: chain D residue  222 SER
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  290 ILE
Chi-restraints excluded: chain D residue  475 SER
Chi-restraints excluded: chain E residue  216 ILE
Chi-restraints excluded: chain E residue  222 SER
Chi-restraints excluded: chain E residue  290 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 116 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 119 optimal weight:    1.9990
   chunk 128 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 147 optimal weight:    4.9990
   chunk 170 optimal weight:    2.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
B  47 GLN
D  26 GLN
D  47 GLN
** E  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  47 GLN
** E 114 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  17270  Z= 0.323
  Angle     :  0.624   6.118  23510  Z= 0.322
  Chirality :  0.042   0.313   2695
  Planarity :  0.005   0.059   2825
  Dihedral  : 10.034  72.075   3383
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 11.79 %
    Favored  : 86.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.94 (0.18), residues: 1960
  helix:  1.70 (0.17), residues: 830
  sheet: -0.32 (0.23), residues: 430
  loop :  0.10 (0.24), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 148 
 HIS   0.003   0.001   HIS E 297 
 PHE   0.015   0.002   PHE A 470 
 TYR   0.016   0.002   TYR A  31 
 ARG   0.008   0.001   ARG C 446 

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

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

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  354 residues out of total 1770 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 329
  time to evaluate  : 2.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6279 (mm-30)
REVERT: A   78 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8222 (mpt-90)
REVERT: B   41 ASP cc_start: 0.7661 (t0) cc_final: 0.7313 (t0)
REVERT: B  450 MET cc_start: 0.5985 (mmm) cc_final: 0.5537 (mmm)
REVERT: C  128 TYR cc_start: 0.7323 (t80) cc_final: 0.7018 (t80)
REVERT: C  294 TYR cc_start: 0.8704 (m-80) cc_final: 0.8380 (m-80)
REVERT: C  472 GLU cc_start: 0.7455 (tt0) cc_final: 0.7046 (tt0)
REVERT: D   97 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6736 (mp0)
REVERT: D  294 TYR cc_start: 0.8606 (m-80) cc_final: 0.8287 (m-80)
REVERT: D  446 ARG cc_start: 0.7851 (tpp80) cc_final: 0.7618 (tpp80)
REVERT: E   44 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.5673 (mm-30)
REVERT: E   92 TYR cc_start: 0.8510 (m-10) cc_final: 0.8244 (m-10)
REVERT: E  216 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7623 (mp)
REVERT: E  455 PHE cc_start: 0.7523 (t80) cc_final: 0.7157 (t80)
  outliers start: 25
  outliers final: 18
  residues processed: 341
  average time/residue: 2.1320
  time to fit residues: 836.5924
Evaluate side-chains
  350 residues out of total 1770 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 327
  time to evaluate  : 2.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 GLU
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  222 SER
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain B residue   69 SER
Chi-restraints excluded: chain B residue   78 ARG
Chi-restraints excluded: chain B residue  216 ILE
Chi-restraints excluded: chain B residue  222 SER
Chi-restraints excluded: chain B residue  238 LYS
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain C residue  290 ILE
Chi-restraints excluded: chain C residue  475 SER
Chi-restraints excluded: chain D residue   97 GLU
Chi-restraints excluded: chain D residue  222 SER
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  290 ILE
Chi-restraints excluded: chain D residue  475 SER
Chi-restraints excluded: chain E residue   44 GLU
Chi-restraints excluded: chain E residue  216 ILE
Chi-restraints excluded: chain E residue  221 ILE
Chi-restraints excluded: chain E residue  222 SER
Chi-restraints excluded: chain E residue  290 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 180 optimal weight:    2.9990
   chunk 164 optimal weight:    0.6980
   chunk 175 optimal weight:    0.9990
   chunk 105 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 137 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 158 optimal weight:    0.3980
   chunk 165 optimal weight:    2.9990
   chunk 174 optimal weight:    0.8980
   chunk 115 optimal weight:    0.9980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B  47 GLN
D  47 GLN
D 106 ASN
E  26 GLN
E  47 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  17270  Z= 0.184
  Angle     :  0.550   9.378  23510  Z= 0.282
  Chirality :  0.040   0.289   2695
  Planarity :  0.004   0.058   2825
  Dihedral  :  9.774  71.458   3383
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 12.12 %
    Favored  : 86.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.13 (0.19), residues: 1960
  helix:  1.88 (0.17), residues: 825
  sheet: -0.17 (0.24), residues: 420
  loop :  0.13 (0.24), residues: 715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 133 
 HIS   0.002   0.001   HIS B 104 
 PHE   0.013   0.001   PHE E 470 
 TYR   0.009   0.001   TYR D 273 
 ARG   0.009   0.001   ARG A 446 

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

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

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  360 residues out of total 1770 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 337
  time to evaluate  : 2.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6262 (mm-30)
REVERT: A   78 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8239 (mpt-90)
REVERT: B   41 ASP cc_start: 0.7658 (t0) cc_final: 0.7274 (t0)
REVERT: B  450 MET cc_start: 0.5912 (mmm) cc_final: 0.5472 (mmm)
REVERT: C  128 TYR cc_start: 0.7318 (t80) cc_final: 0.7009 (t80)
REVERT: C  294 TYR cc_start: 0.8672 (m-80) cc_final: 0.8453 (m-80)
REVERT: C  450 MET cc_start: 0.6826 (ptt) cc_final: 0.6590 (ptt)
REVERT: C  472 GLU cc_start: 0.7395 (tt0) cc_final: 0.7048 (tt0)
REVERT: D   97 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6745 (mp0)
REVERT: D  294 TYR cc_start: 0.8591 (m-80) cc_final: 0.8361 (m-80)
REVERT: D  446 ARG cc_start: 0.7832 (tpp80) cc_final: 0.7602 (tpp80)
REVERT: E  216 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7569 (mp)
REVERT: E  254 LEU cc_start: 0.7568 (mt) cc_final: 0.7347 (mt)
REVERT: E  455 PHE cc_start: 0.7485 (t80) cc_final: 0.7136 (t80)
  outliers start: 23
  outliers final: 18
  residues processed: 348
  average time/residue: 2.1246
  time to fit residues: 851.8593
Evaluate side-chains
  351 residues out of total 1770 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 329
  time to evaluate  : 2.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 GLU
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  222 SER
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain B residue   78 ARG
Chi-restraints excluded: chain B residue  216 ILE
Chi-restraints excluded: chain B residue  222 SER
Chi-restraints excluded: chain B residue  238 LYS
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain C residue  290 ILE
Chi-restraints excluded: chain C residue  475 SER
Chi-restraints excluded: chain D residue   97 GLU
Chi-restraints excluded: chain D residue  221 ILE
Chi-restraints excluded: chain D residue  222 SER
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  290 ILE
Chi-restraints excluded: chain D residue  475 SER
Chi-restraints excluded: chain E residue  216 ILE
Chi-restraints excluded: chain E residue  221 ILE
Chi-restraints excluded: chain E residue  222 SER
Chi-restraints excluded: chain E residue  290 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 185 optimal weight:    0.4980
   chunk 113 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 128 optimal weight:    0.6980
   chunk 194 optimal weight:    1.9990
   chunk 178 optimal weight:    2.9990
   chunk 154 optimal weight:    1.9990
   chunk 16 optimal weight:    0.2980
   chunk 119 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 122 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B  47 GLN
D  26 GLN
D  47 GLN
E  26 GLN
E  47 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  17270  Z= 0.174
  Angle     :  0.533   6.603  23510  Z= 0.274
  Chirality :  0.039   0.290   2695
  Planarity :  0.004   0.061   2825
  Dihedral  :  9.220  74.661   3383
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 12.18 %
    Favored  : 86.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.32 (0.19), residues: 1960
  helix:  2.05 (0.17), residues: 825
  sheet: -0.09 (0.24), residues: 420
  loop :  0.22 (0.24), residues: 715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  66 
 HIS   0.002   0.001   HIS B 104 
 PHE   0.012   0.001   PHE E 470 
 TYR   0.008   0.001   TYR D 419 
 ARG   0.009   0.000   ARG C 446 

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

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

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 1770 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 331
  time to evaluate  : 2.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6242 (mm-30)
REVERT: A   67 ASN cc_start: 0.6205 (t0) cc_final: 0.5726 (m110)
REVERT: A   78 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8263 (mpt-90)
REVERT: A  436 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6769 (mm-30)
REVERT: A  450 MET cc_start: 0.5769 (mmm) cc_final: 0.5061 (mmm)
REVERT: B   41 ASP cc_start: 0.7665 (t0) cc_final: 0.7324 (t0)
REVERT: B   44 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6258 (tm-30)
REVERT: B  450 MET cc_start: 0.5913 (mmm) cc_final: 0.5469 (mmm)
REVERT: C  128 TYR cc_start: 0.7308 (t80) cc_final: 0.6992 (t80)
REVERT: C  294 TYR cc_start: 0.8672 (m-80) cc_final: 0.8442 (m-80)
REVERT: C  322 MET cc_start: 0.7683 (mtp) cc_final: 0.7366 (mtm)
REVERT: C  472 GLU cc_start: 0.7348 (tt0) cc_final: 0.7085 (tt0)
REVERT: D   97 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6735 (mp0)
REVERT: D  294 TYR cc_start: 0.8580 (m-80) cc_final: 0.8372 (m-80)
REVERT: D  446 ARG cc_start: 0.7828 (tpp80) cc_final: 0.7609 (tpp80)
REVERT: E  216 ILE cc_start: 0.7720 (mp) cc_final: 0.7514 (mm)
REVERT: E  254 LEU cc_start: 0.7561 (mt) cc_final: 0.7333 (mt)
REVERT: E  455 PHE cc_start: 0.7477 (t80) cc_final: 0.7139 (t80)
  outliers start: 24
  outliers final: 18
  residues processed: 342
  average time/residue: 2.1138
  time to fit residues: 831.3124
Evaluate side-chains
  344 residues out of total 1770 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 322
  time to evaluate  : 3.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 GLU
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  222 SER
Chi-restraints excluded: chain A residue  436 GLU
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain B residue   78 ARG
Chi-restraints excluded: chain B residue  222 SER
Chi-restraints excluded: chain B residue  238 LYS
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain C residue  290 ILE
Chi-restraints excluded: chain C residue  475 SER
Chi-restraints excluded: chain D residue   67 ASN
Chi-restraints excluded: chain D residue   97 GLU
Chi-restraints excluded: chain D residue  221 ILE
Chi-restraints excluded: chain D residue  222 SER
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  290 ILE
Chi-restraints excluded: chain D residue  475 SER
Chi-restraints excluded: chain E residue  221 ILE
Chi-restraints excluded: chain E residue  222 SER
Chi-restraints excluded: chain E residue  290 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 164 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 142 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 154 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 159 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 136 optimal weight:    0.6980
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
B  26 GLN
B  47 GLN
D  47 GLN
D 106 ASN
E  47 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.152944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.133701 restraints weight = 58816.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 1.40
r_work: 0.3262 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3114
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3114
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  17270  Z= 0.247
  Angle     :  0.583   5.796  23510  Z= 0.301
  Chirality :  0.040   0.259   2695
  Planarity :  0.005   0.061   2825
  Dihedral  :  9.317  79.667   3383
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 12.35 %
    Favored  : 86.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.14 (0.18), residues: 1960
  helix:  1.91 (0.17), residues: 830
  sheet: -0.28 (0.23), residues: 430
  loop :  0.19 (0.24), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 133 
 HIS   0.003   0.001   HIS B 297 
 PHE   0.014   0.002   PHE A 470 
 TYR   0.012   0.002   TYR A  31 
 ARG   0.008   0.001   ARG C 446 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 13587.97 seconds
wall clock time: 240 minutes 8.02 seconds (14408.02 seconds total)