Starting phenix.real_space_refine
on Mon Apr 28 17:23:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jgg_36233/04_2025/8jgg_36233_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jgg_36233/04_2025/8jgg_36233.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jgg_36233/04_2025/8jgg_36233.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jgg_36233/04_2025/8jgg_36233.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jgg_36233/04_2025/8jgg_36233_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jgg_36233/04_2025/8jgg_36233_neut.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.047
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: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    5053      2.51       5
     N    1362      2.21       5
     O    1426      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7889
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "G"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 414
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "L"
      Number of atoms: 102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 102
          Classifications: {'peptide': 11}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'TRANS': 10}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "S"
      Number of atoms: 1690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1690
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 10, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 97
          Unresolved non-hydrogen angles: 119
          Unresolved non-hydrogen dihedrals: 78
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 2, 'TYR:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 63
    Chain: "A"
      Number of atoms: 1599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1599
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 2, 'TRANS': 213}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 146
          Unresolved non-hydrogen angles: 181
          Unresolved non-hydrogen dihedrals: 118
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 98
    Chain: "B"
      Number of atoms: 2436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2436
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 150
          Unresolved non-hydrogen angles: 185
          Unresolved non-hydrogen dihedrals: 119
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 3, 'ASP:plan': 8, 'ASN%COO:plan1': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 118
    Chain: "R"
      Number of atoms: 1648
      Number of conformers: 3
      Conformer: "A"
        Number of residues, atoms: 223, 1640
          Classifications: {'peptide': 223}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 5, 'TRANS': 217}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 154
          Unresolved non-hydrogen angles: 202
          Unresolved non-hydrogen dihedrals: 132
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 76
      Conformer: "B"
        Number of residues, atoms: 223, 1640
          Classifications: {'peptide': 223}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 5, 'TRANS': 217}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 154
          Unresolved non-hydrogen angles: 202
          Unresolved non-hydrogen dihedrals: 132
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 76
          bond proxies already assigned to first conformer: 1673
      Conformer: "C"
        Number of residues, atoms: 223, 1640
          Classifications: {'peptide': 223}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 5, 'TRANS': 217}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 154
          Unresolved non-hydrogen angles: 202
          Unresolved non-hydrogen dihedrals: 132
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 76
          bond proxies already assigned to first conformer: 1673
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AGLY R 276 " occ=0.13
      ... (10 atoms not shown)
      pdb=" O  CGLY R 276 " occ=0.74
  Time building chain proxies: 6.89, per 1000 atoms: 0.87
  Number of scatterers: 7889
  At special positions: 0
  Unit cell: (111.25, 102.35, 125.49, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    1426      8.00
     N    1362      7.00
     C    5053      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.30
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2006

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 13 sheets defined
      34.7% alpha, 21.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'G' and resid 9 through 24
      removed outlier: 3.778A  pdb=" N   LEU G  15 " --> pdb=" O   GLN G  11 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   VAL G  16 " --> pdb=" O   ALA G  12 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLU G  17 " --> pdb=" O   ARG G  13 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.942A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'G' and resid 59 through 64
      removed outlier: 4.542A  pdb=" N   GLU G  63 " --> pdb=" O   ASN G  59 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LYS G  64 " --> pdb=" O   PRO G  60 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 59 through 64'
    Processing helix  chain 'L' and resid 15 through 19
      removed outlier: 4.053A  pdb=" N   LYS L  19 " --> pdb=" O   ASP L  16 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 3.734A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 62 through 65
    Processing helix  chain 'A' and resid 9 through 19
      removed outlier: 3.754A  pdb=" N   VAL A  13 " --> pdb=" O   ASP A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 20 through 31
      removed outlier: 3.821A  pdb=" N   ARG A  24 " --> pdb=" O   ASP A  20 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLU A  25 " --> pdb=" O   ARG A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.593A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 211
    Processing helix  chain 'A' and resid 242 through 255
      removed outlier: 3.644A  pdb=" N   ASN A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 281
      removed outlier: 3.972A  pdb=" N   GLU A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 4.069A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.659A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLN A 306 " --> pdb=" O   TYR A 302 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   PHE A 307 " --> pdb=" O   ILE A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 9 through 25
      removed outlier: 3.676A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'B' and resid 128 through 132
      removed outlier: 4.000A  pdb=" N   GLY B 131 " --> pdb=" O   THR B 128 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   ASN B 132 " --> pdb=" O   ARG B 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 128 through 132'
    Processing helix  chain 'R' and resid 29 through 33
      removed outlier: 3.511A  pdb=" N   LEU R  33 " --> pdb=" O   LEU R  30 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 35 through 52
      removed outlier: 4.301A  pdb=" N   THR R  43 " --> pdb=" O   LEU R  39 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 61 through 84
      removed outlier: 3.524A  pdb=" N   ILE R  65 " --> pdb=" O   PHE R  61 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU R  84 " --> pdb=" O   LEU R  80 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 98 through 126
      removed outlier: 4.124A  pdb=" N   VAL R 124 " --> pdb=" O   ARG R 120 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   TRP R 126 " --> pdb=" O   LEU R 122 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 126 through 133
    Processing helix  chain 'R' and resid 137 through 159
      removed outlier: 3.767A  pdb=" N   LEU R 151 " --> pdb=" O   TRP R 147 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ARG R 153 " --> pdb=" O   LEU R 149 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   MET R 159 " --> pdb=" O   ILE R 155 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 175 through 203
      removed outlier: 3.646A  pdb=" N   ILE R 179 " --> pdb=" O   THR R 175 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU R 203 " --> pdb=" O   LEU R 199 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 213 through 224
      removed outlier: 3.703A  pdb=" N   LEU R 220 " --> pdb=" O   VAL R 216 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 230 through 236
      removed outlier: 3.617A  pdb=" N   GLN R 235 " --> pdb=" O   PRO R 231 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 247 through 251
    Processing helix  chain 'R' and resid 254 through 273
      Proline residue:  R 269  - end of helix
    Processing sheet with id=AA1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'S' and resid 58 through 60
      removed outlier: 6.549A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'S' and resid 128 through 129
    Processing sheet with id=AA4, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.753A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   LEU S 166 " --> pdb=" O   LEU S 175 " (cutoff:3.500A)
      removed outlier: 5.520A  pdb=" N   LEU S 175 " --> pdb=" O   LEU S 166 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.561A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.555A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.741A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.798A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.842A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.060A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.420A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.833A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 5.557A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.850A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   GLY B 202 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 229 through 234
    Processing sheet with id=AB3, first strand: chain 'B' and resid 250 through 254
      removed outlier: 6.637A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.995A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    349 hydrogen bonds defined for protein.
    975 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: 2.23

  Time building geometry restraints manager: 2.56 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1252
        1.30 -     1.43: 2170
        1.43 -     1.56: 4563
        1.56 -     1.68: 1
        1.68 -     1.81: 66
  Bond restraints: 8052
  Sorted by residual:
  bond pdb=" C   HIS B  62 "
       pdb=" O   HIS B  62 "
    ideal  model  delta    sigma   weight residual
    1.234  1.174  0.060 1.22e-02 6.72e+03 2.41e+01
  bond pdb=" CA  GLN B 175 "
       pdb=" C   GLN B 175 "
    ideal  model  delta    sigma   weight residual
    1.524  1.465  0.059 1.31e-02 5.83e+03 2.04e+01
  bond pdb=" C   ASN A 347 "
       pdb=" O   ASN A 347 "
    ideal  model  delta    sigma   weight residual
    1.237  1.186  0.050 1.17e-02 7.31e+03 1.86e+01
  bond pdb=" CA  PHE A 223 "
       pdb=" C   PHE A 223 "
    ideal  model  delta    sigma   weight residual
    1.523  1.472  0.050 1.23e-02 6.61e+03 1.68e+01
  bond pdb=" CA  ASP B  66 "
       pdb=" C   ASP B  66 "
    ideal  model  delta    sigma   weight residual
    1.522  1.468  0.054 1.31e-02 5.83e+03 1.67e+01
  ... (remaining 8047 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.63: 10682
        2.63 -     5.25: 227
        5.25 -     7.88: 34
        7.88 -    10.50: 13
       10.50 -    13.13: 2
  Bond angle restraints: 10958
  Sorted by residual:
  angle pdb=" N   THR R  34 "
        pdb=" CA  THR R  34 "
        pdb=" C   THR R  34 "
      ideal   model   delta    sigma   weight residual
     112.89   99.76   13.13 1.24e+00 6.50e-01 1.12e+02
  angle pdb=" N   HIS R 252 "
        pdb=" CA  HIS R 252 "
        pdb=" C   HIS R 252 "
      ideal   model   delta    sigma   weight residual
     113.55  101.39   12.16 1.26e+00 6.30e-01 9.31e+01
  angle pdb=" N   LYS A  10 "
        pdb=" CA  LYS A  10 "
        pdb=" C   LYS A  10 "
      ideal   model   delta    sigma   weight residual
     113.50  103.02   10.48 1.23e+00 6.61e-01 7.25e+01
  angle pdb=" N   ALA A   7 "
        pdb=" CA  ALA A   7 "
        pdb=" C   ALA A   7 "
      ideal   model   delta    sigma   weight residual
     113.41  103.66    9.75 1.22e+00 6.72e-01 6.39e+01
  angle pdb=" C   TYR S 223 "
        pdb=" N   PRO S 224 "
        pdb=" CA  PRO S 224 "
      ideal   model   delta    sigma   weight residual
     119.76  112.95    6.81 1.00e+00 1.00e+00 4.63e+01
  ... (remaining 10953 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.24: 4100
       16.24 -    32.49: 439
       32.49 -    48.73: 121
       48.73 -    64.98: 21
       64.98 -    81.22: 3
  Dihedral angle restraints: 4684
    sinusoidal: 1578
      harmonic: 3106
  Sorted by residual:
  dihedral pdb=" CA  THR B 165 "
           pdb=" C   THR B 165 "
           pdb=" N   CYS B 166 "
           pdb=" CA  CYS B 166 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.02   17.98     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  TRP B 169 "
           pdb=" C   TRP B 169 "
           pdb=" N   ASP B 170 "
           pdb=" CA  ASP B 170 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.19   17.81     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  HIS S  35 "
           pdb=" C   HIS S  35 "
           pdb=" N   TRP S  36 "
           pdb=" CA  TRP S  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.79   16.21     0      5.00e+00 4.00e-02 1.05e+01
  ... (remaining 4681 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1123
       0.073 -    0.146: 147
       0.146 -    0.220: 17
       0.220 -    0.293: 1
       0.293 -    0.366: 3
  Chirality restraints: 1291
  Sorted by residual:
  chirality pdb=" CA  LEU A 348 "
            pdb=" N   LEU A 348 "
            pdb=" C   LEU A 348 "
            pdb=" CB  LEU A 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.35e+00
  chirality pdb=" CA  ILE A 184 "
            pdb=" N   ILE A 184 "
            pdb=" C   ILE A 184 "
            pdb=" CB  ILE A 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.74   -0.30 2.00e-01 2.50e+01 2.29e+00
  chirality pdb=" CA  HIS R 254 "
            pdb=" N   HIS R 254 "
            pdb=" C   HIS R 254 "
            pdb=" CB  HIS R 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.29e+00
  ... (remaining 1288 not shown)

  Planarity restraints: 1374
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS L  19 "    0.012 2.00e-02 2.50e+03   2.45e-02 5.98e+00
        pdb=" C   LYS L  19 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   LYS L  19 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ARG L  20 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 348 "    0.012 2.00e-02 2.50e+03   2.30e-02 5.31e+00
        pdb=" C   LEU A 348 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   LEU A 348 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LYS A 349 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 232 "   -0.010 2.00e-02 2.50e+03   2.08e-02 4.35e+00
        pdb=" C   ILE B 232 "    0.036 2.00e-02 2.50e+03
        pdb=" O   ILE B 232 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   CYS B 233 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1371 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2391
        2.81 -     3.33: 6758
        3.33 -     3.86: 12570
        3.86 -     4.38: 14371
        4.38 -     4.90: 25872
  Nonbonded interactions: 61962
  Sorted by model distance:
  nonbonded pdb=" OG  SER S 134 "
            pdb=" OE2 GLU S 234 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" O   LEU B  30 "
            pdb=" OG1 THR B  34 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" ND2 ASN B 230 "
            pdb=" OD1 ASP B 246 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" O   VAL R 253 "
            pdb=" OG  SER R 257 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" N   GLY B 185 "
            pdb=" OD1 ASP B 205 "
     model   vdw
     2.346 3.120
  ... (remaining 61957 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.13 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.600
  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:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.700
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:15.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
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      :  0.006   0.076   8053  Z= 0.441
  Angle     :  0.941  13.129  10960  Z= 0.605
  Chirality :  0.052   0.366   1291
  Planarity :  0.004   0.042   1374
  Dihedral  : 14.774  81.222   2675
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 24.47 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.25), residues: 1054
  helix:  0.24 (0.31), residues: 314
  sheet: -0.45 (0.31), residues: 273
  loop : -2.24 (0.26), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP L  13 
 HIS   0.009   0.001   HIS B 183 
 PHE   0.015   0.001   PHE S  68 
 TYR   0.018   0.001   TYR S  60 
 ARG   0.003   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17875 (  349)
  hydrogen bonds       : angle       6.79797 (  975)
  SS BOND              : bond        0.00347 (    1)
  SS BOND              : angle       0.72833 (    2)
  covalent geometry    : bond        0.00627 ( 8052)
  covalent geometry    : angle       0.94132 (10958)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7383 (mt-10)
REVERT: B  186 ASP cc_start: 0.7487 (p0) cc_final: 0.6904 (p0)
REVERT: R   79 ARG cc_start: 0.7649 (mmp80) cc_final: 0.7438 (mmp-170)
REVERT: R  254 HIS cc_start: 0.3545 (OUTLIER) cc_final: 0.2345 (t-90)
  outliers start: 8
  outliers final: 4
  residues processed: 119
  average time/residue: 1.0179
  time to fit residues: 130.4241
Evaluate side-chains
  98 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 93
  time to evaluate  : 1.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  250 PHE
Chi-restraints excluded: chain R residue  254 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    0.0170
   chunk 79 optimal weight:    3.9990
   chunk 44 optimal weight:   20.0000
   chunk 27 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 82 optimal weight:    0.7980
   chunk 31 optimal weight:    4.9990
   chunk 50 optimal weight:   20.0000
   chunk 61 optimal weight:    2.9990
   chunk 95 optimal weight:    0.7980
   overall best weight:    0.8820

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.174708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.122335 restraints weight = 9551.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 2.70
r_work: 0.3307 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3161
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3161
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.1198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8053  Z= 0.117
  Angle     :  0.530   8.848  10960  Z= 0.281
  Chirality :  0.042   0.138   1291
  Planarity :  0.004   0.044   1374
  Dihedral  :  5.057  53.218   1153
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 24.47 %
    Favored  : 72.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.26), residues: 1054
  helix:  1.04 (0.31), residues: 322
  sheet: -0.17 (0.30), residues: 274
  loop : -1.92 (0.26), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 183 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.020   0.001   PHE A 189 
 TYR   0.015   0.001   TYR S 178 
 ARG   0.002   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04180 (  349)
  hydrogen bonds       : angle       4.77001 (  975)
  SS BOND              : bond        0.00580 (    1)
  SS BOND              : angle       0.97054 (    2)
  covalent geometry    : bond        0.00257 ( 8052)
  covalent geometry    : angle       0.53020 (10958)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7479 (mm-30)
REVERT: B  134 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7653 (mtm110)
REVERT: B  146 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8177 (mp)
REVERT: R  173 CYS cc_start: 0.6197 (t) cc_final: 0.5203 (m)
REVERT: R  242 ILE cc_start: 0.8454 (pp) cc_final: 0.8086 (pt)
  outliers start: 24
  outliers final: 9
  residues processed: 130
  average time/residue: 1.0892
  time to fit residues: 151.1308
Evaluate side-chains
  117 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   52 SER
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  231 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain R residue  103 MET
Chi-restraints excluded: chain R residue  250 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 80 optimal weight:    8.9990
   chunk 31 optimal weight:    0.5980
   chunk 12 optimal weight:    6.9990
   chunk 75 optimal weight:    4.9990
   chunk 44 optimal weight:   20.0000
   chunk 78 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 103 optimal weight:   10.0000
   chunk 7 optimal weight:    7.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 304 GLN
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.171225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.117969 restraints weight = 9680.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 2.71
r_work: 0.3252 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3107
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3107
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8053  Z= 0.184
  Angle     :  0.581   9.338  10960  Z= 0.304
  Chirality :  0.043   0.136   1291
  Planarity :  0.004   0.046   1374
  Dihedral  :  4.716  48.787   1147
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 24.21 %
    Favored  : 71.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.26), residues: 1054
  helix:  1.11 (0.31), residues: 321
  sheet: -0.18 (0.30), residues: 277
  loop : -1.79 (0.27), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  63 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.021   0.002   PHE B 151 
 TYR   0.013   0.002   TYR S 178 
 ARG   0.003   0.000   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04481 (  349)
  hydrogen bonds       : angle       4.64085 (  975)
  SS BOND              : bond        0.00756 (    1)
  SS BOND              : angle       1.42773 (    2)
  covalent geometry    : bond        0.00436 ( 8052)
  covalent geometry    : angle       0.58096 (10958)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 103
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7639 (mt-10)
REVERT: B  134 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7638 (mtm110)
REVERT: B  186 ASP cc_start: 0.7551 (p0) cc_final: 0.6925 (p0)
REVERT: R   73 PHE cc_start: 0.7466 (t80) cc_final: 0.7242 (t80)
REVERT: R  173 CYS cc_start: 0.6102 (t) cc_final: 0.5168 (m)
  outliers start: 30
  outliers final: 14
  residues processed: 125
  average time/residue: 1.0871
  time to fit residues: 144.9971
Evaluate side-chains
  110 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   52 SER
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  231 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  103 MET
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  250 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 70 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 101 optimal weight:    6.9990
   chunk 76 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 1 optimal weight:   10.0000
   chunk 79 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9980
   chunk 78 optimal weight:    0.8980
   chunk 100 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 304 GLN
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.173833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.120875 restraints weight = 9554.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.71
r_work: 0.3290 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3144
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3144 r_free = 0.3144    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3144 r_free = 0.3144    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3144
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8053  Z= 0.110
  Angle     :  0.509   7.577  10960  Z= 0.266
  Chirality :  0.041   0.134   1291
  Planarity :  0.003   0.046   1374
  Dihedral  :  4.307  47.528   1147
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 25.26 %
    Favored  : 71.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.26), residues: 1054
  helix:  1.39 (0.31), residues: 322
  sheet:  0.05 (0.31), residues: 273
  loop : -1.69 (0.27), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP S  47 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.015   0.001   PHE R 104 
 TYR   0.014   0.001   TYR R  99 
 ARG   0.002   0.000   ARG R 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03742 (  349)
  hydrogen bonds       : angle       4.34093 (  975)
  SS BOND              : bond        0.00716 (    1)
  SS BOND              : angle       1.30485 (    2)
  covalent geometry    : bond        0.00245 ( 8052)
  covalent geometry    : angle       0.50921 (10958)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7544 (mt-10)
REVERT: B  134 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7713 (mtm110)
REVERT: R   73 PHE cc_start: 0.7448 (t80) cc_final: 0.7226 (t80)
REVERT: R  173 CYS cc_start: 0.6162 (t) cc_final: 0.5303 (m)
  outliers start: 27
  outliers final: 14
  residues processed: 119
  average time/residue: 1.1582
  time to fit residues: 147.1513
Evaluate side-chains
  110 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   21 TYR
Chi-restraints excluded: chain S residue  134 SER
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  250 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 71 optimal weight:    7.9990
   chunk 1 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 101 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 50 optimal weight:    8.9990
   chunk 0 optimal weight:    9.9990
   chunk 100 optimal weight:    0.9990
   chunk 7 optimal weight:   10.0000
   chunk 92 optimal weight:    0.3980
   overall best weight:    2.2788

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.170487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.117220 restraints weight = 9558.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 2.70
r_work: 0.3244 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3099
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3099 r_free = 0.3099    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3099 r_free = 0.3099    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3099
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8053  Z= 0.196
  Angle     :  0.584   9.656  10960  Z= 0.304
  Chirality :  0.044   0.137   1291
  Planarity :  0.004   0.048   1374
  Dihedral  :  4.609  46.966   1147
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 25.13 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.26), residues: 1054
  helix:  1.30 (0.31), residues: 321
  sheet: -0.12 (0.30), residues: 278
  loop : -1.71 (0.27), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  63 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.023   0.002   PHE B 151 
 TYR   0.012   0.002   TYR S 178 
 ARG   0.003   0.000   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04341 (  349)
  hydrogen bonds       : angle       4.51577 (  975)
  SS BOND              : bond        0.00813 (    1)
  SS BOND              : angle       1.59961 (    2)
  covalent geometry    : bond        0.00472 ( 8052)
  covalent geometry    : angle       0.58390 (10958)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 95
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
REVERT: S   38 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7875 (ptt180)
REVERT: S  128 MET cc_start: 0.8447 (tpp) cc_final: 0.8209 (mmm)
REVERT: A   33 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7679 (mt-10)
REVERT: B  134 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7621 (mtm110)
REVERT: R   73 PHE cc_start: 0.7469 (t80) cc_final: 0.7268 (t80)
REVERT: R  173 CYS cc_start: 0.6127 (t) cc_final: 0.5267 (m)
  outliers start: 37
  outliers final: 18
  residues processed: 124
  average time/residue: 1.1359
  time to fit residues: 150.1598
Evaluate side-chains
  111 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   21 TYR
Chi-restraints excluded: chain S residue   38 ARG
Chi-restraints excluded: chain S residue  134 SER
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  103 MET
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  250 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 67 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 102 optimal weight:   20.0000
   chunk 98 optimal weight:    8.9990
   chunk 57 optimal weight:    0.6980
   chunk 104 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 90 optimal weight:    0.0970
   overall best weight:    1.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.171477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.118252 restraints weight = 9494.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 2.69
r_work: 0.3253 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3113 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3116
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3116 r_free = 0.3116    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3116 r_free = 0.3116    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3116
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8053  Z= 0.156
  Angle     :  0.544   7.921  10960  Z= 0.285
  Chirality :  0.042   0.135   1291
  Planarity :  0.004   0.047   1374
  Dihedral  :  4.447  45.678   1147
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 25.79 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.26), residues: 1054
  helix:  1.47 (0.31), residues: 321
  sheet: -0.08 (0.30), residues: 284
  loop : -1.68 (0.27), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  63 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.019   0.002   PHE B 151 
 TYR   0.012   0.001   TYR S 178 
 ARG   0.002   0.000   ARG R 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04032 (  349)
  hydrogen bonds       : angle       4.37371 (  975)
  SS BOND              : bond        0.00826 (    1)
  SS BOND              : angle       1.57934 (    2)
  covalent geometry    : bond        0.00372 ( 8052)
  covalent geometry    : angle       0.54378 (10958)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 87
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S  128 MET cc_start: 0.8404 (tpp) cc_final: 0.8188 (mmm)
REVERT: A   33 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7634 (mt-10)
REVERT: B  118 ASP cc_start: 0.6541 (OUTLIER) cc_final: 0.6303 (p0)
REVERT: B  134 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7666 (mtm110)
REVERT: R   79 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.6468 (tpm-80)
REVERT: R  173 CYS cc_start: 0.6066 (t) cc_final: 0.5247 (m)
  outliers start: 32
  outliers final: 19
  residues processed: 114
  average time/residue: 1.0371
  time to fit residues: 126.5925
Evaluate side-chains
  111 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   21 TYR
Chi-restraints excluded: chain S residue  134 SER
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   79 ARG
Chi-restraints excluded: chain R residue  103 MET
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  250 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 88 optimal weight:    9.9990
   chunk 12 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 92 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 53 optimal weight:    8.9990
   chunk 80 optimal weight:    8.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.170674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.117503 restraints weight = 9565.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 2.69
r_work: 0.3234 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3092 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3101
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3101
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.2023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8053  Z= 0.172
  Angle     :  0.560   8.681  10960  Z= 0.294
  Chirality :  0.043   0.135   1291
  Planarity :  0.004   0.048   1374
  Dihedral  :  4.513  44.585   1147
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 26.32 %
    Favored  : 69.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.26), residues: 1054
  helix:  1.47 (0.31), residues: 321
  sheet: -0.18 (0.29), residues: 290
  loop : -1.64 (0.27), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  63 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.021   0.002   PHE B 151 
 TYR   0.012   0.002   TYR S 178 
 ARG   0.002   0.000   ARG R 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04156 (  349)
  hydrogen bonds       : angle       4.39944 (  975)
  SS BOND              : bond        0.00794 (    1)
  SS BOND              : angle       1.58249 (    2)
  covalent geometry    : bond        0.00412 ( 8052)
  covalent geometry    : angle       0.55943 (10958)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 89
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   38 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7824 (ptt180)
REVERT: S  128 MET cc_start: 0.8444 (tpp) cc_final: 0.8183 (mmm)
REVERT: A   33 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7685 (mt-10)
REVERT: B  118 ASP cc_start: 0.6513 (OUTLIER) cc_final: 0.6242 (p0)
REVERT: B  134 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7699 (mtm110)
REVERT: R   79 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.6472 (tpm-80)
REVERT: R  173 CYS cc_start: 0.6040 (t) cc_final: 0.5245 (m)
  outliers start: 32
  outliers final: 21
  residues processed: 115
  average time/residue: 1.0743
  time to fit residues: 132.1103
Evaluate side-chains
  114 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 88
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   21 TYR
Chi-restraints excluded: chain S residue   38 ARG
Chi-restraints excluded: chain S residue  134 SER
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   79 ARG
Chi-restraints excluded: chain R residue   98 LEU
Chi-restraints excluded: chain R residue  103 MET
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  250 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 89 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 34 optimal weight:    4.9990
   chunk 9 optimal weight:    7.9990
   chunk 1 optimal weight:    8.9990
   chunk 8 optimal weight:    8.9990
   chunk 37 optimal weight:    0.4980
   chunk 35 optimal weight:    4.9990
   chunk 99 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.171452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.118095 restraints weight = 9652.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 2.71
r_work: 0.3242 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3110
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3110
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8053  Z= 0.154
  Angle     :  0.548   7.975  10960  Z= 0.284
  Chirality :  0.042   0.135   1291
  Planarity :  0.003   0.047   1374
  Dihedral  :  4.411  44.045   1147
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 26.58 %
    Favored  : 69.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.26), residues: 1054
  helix:  1.57 (0.31), residues: 321
  sheet: -0.12 (0.29), residues: 290
  loop : -1.61 (0.27), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP S  47 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.019   0.002   PHE B 151 
 TYR   0.013   0.002   TYR S 178 
 ARG   0.002   0.000   ARG R 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04015 (  349)
  hydrogen bonds       : angle       4.33702 (  975)
  SS BOND              : bond        0.00776 (    1)
  SS BOND              : angle       1.52752 (    2)
  covalent geometry    : bond        0.00367 ( 8052)
  covalent geometry    : angle       0.54791 (10958)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 88
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   38 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7812 (ptt180)
REVERT: S  128 MET cc_start: 0.8430 (tpp) cc_final: 0.8177 (mmm)
REVERT: A   33 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7645 (mt-10)
REVERT: B  118 ASP cc_start: 0.6482 (OUTLIER) cc_final: 0.6251 (p0)
REVERT: B  134 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7710 (mtm110)
REVERT: R   79 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.6439 (tpm-80)
REVERT: R  173 CYS cc_start: 0.5995 (t) cc_final: 0.5207 (m)
  outliers start: 32
  outliers final: 19
  residues processed: 112
  average time/residue: 1.1377
  time to fit residues: 136.3363
Evaluate side-chains
  113 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   21 TYR
Chi-restraints excluded: chain S residue   38 ARG
Chi-restraints excluded: chain S residue  134 SER
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   79 ARG
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  250 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 80 optimal weight:    6.9990
   chunk 67 optimal weight:    6.9990
   chunk 101 optimal weight:    7.9990
   chunk 82 optimal weight:    0.5980
   chunk 94 optimal weight:    0.3980
   chunk 59 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0270
   chunk 20 optimal weight:   10.0000
   chunk 55 optimal weight:    0.5980
   chunk 97 optimal weight:    0.7980
   chunk 84 optimal weight:    8.9990
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.175429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.123287 restraints weight = 9658.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 2.62
r_work: 0.3319 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3186
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3186
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050   8053  Z= 0.090
  Angle     :  0.484   7.919  10960  Z= 0.249
  Chirality :  0.041   0.142   1291
  Planarity :  0.003   0.044   1374
  Dihedral  :  3.895  41.958   1147
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 28.16 %
    Favored  : 69.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.26), residues: 1054
  helix:  1.70 (0.31), residues: 326
  sheet:  0.14 (0.30), residues: 279
  loop : -1.60 (0.27), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP S  47 
 HIS   0.003   0.000   HIS S  35 
 PHE   0.013   0.001   PHE R 104 
 TYR   0.015   0.001   TYR R  99 
 ARG   0.002   0.000   ARG R 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03256 (  349)
  hydrogen bonds       : angle       4.06205 (  975)
  SS BOND              : bond        0.00557 (    1)
  SS BOND              : angle       1.10227 (    2)
  covalent geometry    : bond        0.00197 ( 8052)
  covalent geometry    : angle       0.48358 (10958)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.807 
Fit side-chains
REVERT: L   20 ARG cc_start: 0.7333 (mtm180) cc_final: 0.6915 (mpp-170)
REVERT: S   38 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7800 (ptt180)
REVERT: A   18 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8144 (ttt)
REVERT: A   33 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7420 (mm-30)
REVERT: R  173 CYS cc_start: 0.5971 (t) cc_final: 0.5243 (m)
  outliers start: 19
  outliers final: 12
  residues processed: 106
  average time/residue: 1.0597
  time to fit residues: 120.0592
Evaluate side-chains
  105 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 1.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   38 ARG
Chi-restraints excluded: chain S residue  134 SER
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 53 optimal weight:    6.9990
   chunk 9 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9980
   chunk 44 optimal weight:   20.0000
   chunk 11 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 67 optimal weight:    7.9990
   chunk 17 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   chunk 84 optimal weight:    9.9990
   chunk 29 optimal weight:    0.5980
   overall best weight:    2.4784

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.170142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.116974 restraints weight = 9581.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 2.68
r_work: 0.3230 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3096
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3096
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   8053  Z= 0.208
  Angle     :  0.588   9.500  10960  Z= 0.307
  Chirality :  0.044   0.137   1291
  Planarity :  0.004   0.046   1374
  Dihedral  :  4.186  19.233   1145
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 28.95 %
    Favored  : 68.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.26), residues: 1054
  helix:  1.49 (0.31), residues: 326
  sheet: -0.07 (0.30), residues: 290
  loop : -1.64 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP S  47 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.024   0.002   PHE B 151 
 TYR   0.013   0.002   TYR S 178 
 ARG   0.003   0.000   ARG B 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04288 (  349)
  hydrogen bonds       : angle       4.39131 (  975)
  SS BOND              : bond        0.00783 (    1)
  SS BOND              : angle       1.59345 (    2)
  covalent geometry    : bond        0.00506 ( 8052)
  covalent geometry    : angle       0.58810 (10958)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
REVERT: S   38 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7783 (ptt180)
REVERT: S  128 MET cc_start: 0.8672 (mmm) cc_final: 0.8105 (mmm)
REVERT: A   33 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7640 (mt-10)
REVERT: R  173 CYS cc_start: 0.5988 (t) cc_final: 0.5223 (m)
  outliers start: 17
  outliers final: 10
  residues processed: 100
  average time/residue: 1.1764
  time to fit residues: 125.4175
Evaluate side-chains
  99 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   21 TYR
Chi-restraints excluded: chain S residue   38 ARG
Chi-restraints excluded: chain S residue  134 SER
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 71 optimal weight:    6.9990
   chunk 22 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 3 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 37 optimal weight:    0.1980
   chunk 27 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.172350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.119828 restraints weight = 9633.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 2.61
r_work: 0.3276 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3141
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3141 r_free = 0.3141    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3141 r_free = 0.3141    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3141
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8053  Z= 0.126
  Angle     :  0.528   7.905  10960  Z= 0.274
  Chirality :  0.042   0.134   1291
  Planarity :  0.003   0.045   1374
  Dihedral  :  3.954  18.333   1145
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 28.68 %
    Favored  : 68.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.26), residues: 1054
  helix:  1.61 (0.31), residues: 326
  sheet: -0.01 (0.30), residues: 290
  loop : -1.59 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP S  47 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.015   0.001   PHE R 104 
 TYR   0.012   0.001   TYR S 178 
 ARG   0.002   0.000   ARG R 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03735 (  349)
  hydrogen bonds       : angle       4.24866 (  975)
  SS BOND              : bond        0.00700 (    1)
  SS BOND              : angle       1.36111 (    2)
  covalent geometry    : bond        0.00295 ( 8052)
  covalent geometry    : angle       0.52766 (10958)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7042.30 seconds
wall clock time: 121 minutes 22.98 seconds (7282.98 seconds total)