Starting phenix.real_space_refine
on Fri Feb 14 16:32:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f6e_28881/02_2025/8f6e_28881.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f6e_28881/02_2025/8f6e_28881.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8f6e_28881/02_2025/8f6e_28881.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f6e_28881/02_2025/8f6e_28881.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f6e_28881/02_2025/8f6e_28881.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f6e_28881/02_2025/8f6e_28881.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.056
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      8      6.06       5
     S      28      5.16       5
     C    6678      2.51       5
     N    1760      2.21       5
     O    2004      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10478
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2172
          Classifications: {'peptide': 282}
          Link IDs: {'PTRANS': 6, 'TRANS': 275}
    Chain: "C"
      Number of atoms: 1474
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1474
          Classifications: {'peptide': 192}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1589
          Classifications: {'peptide': 209}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2172
          Classifications: {'peptide': 282}
          Link IDs: {'PTRANS': 6, 'TRANS': 275}
    Chain: "E"
      Number of atoms: 1474
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1474
          Classifications: {'peptide': 192}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1589
          Classifications: {'peptide': 209}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' ZN': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' ZN': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 6.82, per 1000 atoms: 0.65
  Number of scatterers: 10478
  At special positions: 0
  Unit cell: (67.284, 156.996, 144.18, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      8     29.99
     S      28     16.00
     O    2004      8.00
     N    1760      7.00
     C    6678      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  24 " - pdb=" SG  CYS C  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 136 " - pdb=" SG  CYS C 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  25 " - pdb=" SG  CYS D  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  24 " - pdb=" SG  CYS E  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 136 " - pdb=" SG  CYS E 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  25 " - pdb=" SG  CYS F  99 " 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: 2.54
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 301 "
        pdb="ZN    ZN A 301 " - pdb=" ND1 HIS A 250 "
        pdb="ZN    ZN A 301 " - pdb=" NE2 HIS A 234 "
      pdb="  ZN A 302 "
        pdb="ZN    ZN A 302 " - pdb=" ND1 HIS A  73 "
        pdb="ZN    ZN A 302 " - pdb=" NE2 HIS A  77 "
      pdb="  ZN A 303 "
        pdb="ZN    ZN A 303 " - pdb=" NE2 HIS A 155 "
      pdb="  ZN A 304 "
        pdb="ZN    ZN A 304 " - pdb=" NE2 HIS B 263 "
        pdb="ZN    ZN A 304 " - pdb=" NE2 HIS A 285 "
      pdb="  ZN B 301 "
        pdb="ZN    ZN B 301 " - pdb=" NE2 HIS A 263 "
        pdb="ZN    ZN B 301 " - pdb=" NE2 HIS B 285 "
      pdb="  ZN B 302 "
        pdb="ZN    ZN B 302 " - pdb=" ND1 HIS B 250 "
        pdb="ZN    ZN B 302 " - pdb=" NE2 HIS B 234 "
      pdb="  ZN B 303 "
        pdb="ZN    ZN B 303 " - pdb=" ND1 HIS B  73 "
        pdb="ZN    ZN B 303 " - pdb=" NE2 HIS B  77 "
      pdb="  ZN B 304 "
        pdb="ZN    ZN B 304 " - pdb=" NE2 HIS B 155 "


  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2560

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 23 sheets defined
      31.8% alpha, 22.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 32
      removed outlier: 3.565A  pdb=" N   SER A  18 " --> pdb=" O   ALA A  14 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   THR A  24 " --> pdb=" O   ALA A  20 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE A  26 " --> pdb=" O   ALA A  22 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ILE A  28 " --> pdb=" O   THR A  24 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   LYS A  29 " --> pdb=" O   LEU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 67
      removed outlier: 4.067A  pdb=" N   LEU A  42 " --> pdb=" O   SER A  38 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ALA A  43 " --> pdb=" O   ALA A  39 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   VAL A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 109
      removed outlier: 3.613A  pdb=" N   ALA A  87 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   PHE A 101 " --> pdb=" O   PHE A  97 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLY A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLY A 104 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 142
      removed outlier: 3.723A  pdb=" N   VAL A 120 " --> pdb=" O   ALA A 116 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   VAL A 121 " --> pdb=" O   THR A 117 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   VAL A 125 " --> pdb=" O   VAL A 121 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ALA A 126 " --> pdb=" O   VAL A 122 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE A 127 " --> pdb=" O   SER A 123 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   ALA A 132 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   LEU A 133 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL A 134 " --> pdb=" O   THR A 130 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   LEU A 135 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   LYS A 138 " --> pdb=" O   VAL A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 175
      removed outlier: 3.529A  pdb=" N   SER A 153 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LEU A 154 " --> pdb=" O   GLU A 150 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   HIS A 155 " --> pdb=" O   ALA A 151 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   LEU A 160 " --> pdb=" O   TYR A 156 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   PHE A 161 " --> pdb=" O   LYS A 157 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   VAL A 166 " --> pdb=" O   LEU A 162 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LEU A 167 " --> pdb=" O   ASN A 163 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU A 172 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 208
      removed outlier: 3.600A  pdb=" N   TYR A 191 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ILE A 192 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ARG A 202 " --> pdb=" O   ASP A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 222
      removed outlier: 3.758A  pdb=" N   ARG A 219 " --> pdb=" O   ASP A 215 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ILE A 220 " --> pdb=" O   THR A 216 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LYS A 221 " --> pdb=" O   ARG A 217 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU A 222 " --> pdb=" O   GLN A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 277
      removed outlier: 3.655A  pdb=" N   SER A 264 " --> pdb=" O   ASN A 260 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ILE A 265 " --> pdb=" O   GLU A 261 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   THR A 266 " --> pdb=" O   ALA A 262 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   LEU A 271 " --> pdb=" O   ASP A 267 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LYS A 274 " --> pdb=" O   GLY A 270 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   ALA A 275 " --> pdb=" O   LEU A 271 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   PHE A 277 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 124 through 130
      removed outlier: 4.200A  pdb=" N   LYS C 128 " --> pdb=" O   ASP C 124 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   SER C 129 " --> pdb=" O   SER C 125 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   GLY C 130 " --> pdb=" O   GLN C 126 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 124 through 130'
    Processing helix  chain 'C' and resid 184 through 190
      removed outlier: 3.641A  pdb=" N   GLU C 189 " --> pdb=" O   LYS C 185 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   LYS C 190 " --> pdb=" O   ALA C 186 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 94
      removed outlier: 3.983A  pdb=" N   THR D  94 " --> pdb=" O   ALA D  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 34
      removed outlier: 3.507A  pdb=" N   SER B  18 " --> pdb=" O   ALA B  14 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   THR B  24 " --> pdb=" O   ALA B  20 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ILE B  26 " --> pdb=" O   ALA B  22 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ILE B  28 " --> pdb=" O   THR B  24 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   LYS B  29 " --> pdb=" O   LEU B  25 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   LEU B  34 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 39 through 67
      removed outlier: 3.954A  pdb=" N   ALA B  43 " --> pdb=" O   ALA B  39 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   SER B  44 " --> pdb=" O   SER B  40 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   VAL B  67 " --> pdb=" O   ARG B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 109
      removed outlier: 3.668A  pdb=" N   ALA B  87 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ILE B  92 " --> pdb=" O   GLN B  88 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   PHE B 101 " --> pdb=" O   PHE B  97 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLY B 103 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLY B 104 " --> pdb=" O   LEU B 100 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLU B 105 " --> pdb=" O   PHE B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 142
      removed outlier: 3.561A  pdb=" N   GLY B 119 " --> pdb=" O   ASN B 115 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   VAL B 125 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ALA B 126 " --> pdb=" O   VAL B 122 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ILE B 127 " --> pdb=" O   SER B 123 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ALA B 132 " --> pdb=" O   VAL B 128 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   LEU B 133 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   VAL B 134 " --> pdb=" O   THR B 130 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   LEU B 135 " --> pdb=" O   LEU B 131 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   LYS B 138 " --> pdb=" O   VAL B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 175
      removed outlier: 3.667A  pdb=" N   LEU B 154 " --> pdb=" O   GLU B 150 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   HIS B 155 " --> pdb=" O   ALA B 151 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LEU B 160 " --> pdb=" O   TYR B 156 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   PHE B 161 " --> pdb=" O   LYS B 157 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   VAL B 166 " --> pdb=" O   LEU B 162 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LEU B 167 " --> pdb=" O   ASN B 163 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU B 172 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 208
      removed outlier: 4.061A  pdb=" N   ASP B 181 " --> pdb=" O   TRP B 177 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   GLY B 182 " --> pdb=" O   TRP B 178 " (cutoff:3.500A)
      removed outlier: 4.890A  pdb=" N   LEU B 183 " --> pdb=" O   TRP B 179 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   TYR B 191 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ILE B 192 " --> pdb=" O   ILE B 188 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ARG B 202 " --> pdb=" O   ASP B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 222
      removed outlier: 3.798A  pdb=" N   ARG B 219 " --> pdb=" O   ASP B 215 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ILE B 220 " --> pdb=" O   THR B 216 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LYS B 221 " --> pdb=" O   ARG B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 277
      removed outlier: 3.650A  pdb=" N   SER B 264 " --> pdb=" O   ASN B 260 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ILE B 265 " --> pdb=" O   GLU B 261 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   THR B 266 " --> pdb=" O   ALA B 262 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU B 271 " --> pdb=" O   ASP B 267 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LYS B 274 " --> pdb=" O   GLY B 270 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   ALA B 275 " --> pdb=" O   LEU B 271 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ALA B 276 " --> pdb=" O   ARG B 272 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   PHE B 277 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 124 through 130
      removed outlier: 4.234A  pdb=" N   LYS E 128 " --> pdb=" O   ASP E 124 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   SER E 129 " --> pdb=" O   SER E 125 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   GLY E 130 " --> pdb=" O   GLN E 126 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 124 through 130'
    Processing helix  chain 'E' and resid 184 through 190
      removed outlier: 3.654A  pdb=" N   GLU E 189 " --> pdb=" O   LYS E 185 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   LYS E 190 " --> pdb=" O   ALA E 186 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 90 through 94
      removed outlier: 3.975A  pdb=" N   THR F  94 " --> pdb=" O   ALA F  91 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 232 through 234
      removed outlier: 3.808A  pdb=" N   GLY A 232 " --> pdb=" O   GLU A 252 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLU A 252 " --> pdb=" O   GLY A 232 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   HIS A 234 " --> pdb=" O   HIS A 250 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 234
      removed outlier: 3.808A  pdb=" N   GLY A 232 " --> pdb=" O   GLU A 252 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLU A 252 " --> pdb=" O   GLY A 232 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   HIS A 234 " --> pdb=" O   HIS A 250 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   PHE A 249 " --> pdb=" O   ILE A 283 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 12 through 13
      removed outlier: 3.977A  pdb=" N   GLU C 107 " --> pdb=" O   LEU C  12 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ILE C  49 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   GLN C  38 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   LEU C  47 " --> pdb=" O   GLN C  38 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 20 through 25
      removed outlier: 3.801A  pdb=" N   VAL C  20 " --> pdb=" O   ILE C  76 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ILE C  76 " --> pdb=" O   VAL C  20 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   THR C  73 " --> pdb=" O   SER C  66 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 90 through 91
      removed outlier: 3.879A  pdb=" N   THR C  99 " --> pdb=" O   GLN C  91 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 116 through 119
    Processing sheet with id=AA7, first strand: chain 'D' and resid 6 through 10
      removed outlier: 3.508A  pdb=" N   VAL D   8 " --> pdb=" O   ALA D  26 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 48 through 54
      removed outlier: 7.062A  pdb=" N   TRP D  39 " --> pdb=" O   VAL D  51 " (cutoff:3.500A)
      removed outlier: 4.983A  pdb=" N   SER D  53 " --> pdb=" O   ILE D  37 " (cutoff:3.500A)
      removed outlier: 7.276A  pdb=" N   ILE D  37 " --> pdb=" O   SER D  53 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 71 through 76
      removed outlier: 3.879A  pdb=" N   THR D  81 " --> pdb=" O   ASP D  76 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 106 through 107
    Processing sheet with id=AB2, first strand: chain 'D' and resid 137 through 141
      removed outlier: 3.537A  pdb=" N   LYS D 160 " --> pdb=" O   SER D 137 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLY D 156 " --> pdb=" O   LEU D 141 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ASP D 161 " --> pdb=" O   TYR D 193 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   TYR D 193 " --> pdb=" O   ASP D 161 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 137 through 141
      removed outlier: 3.537A  pdb=" N   LYS D 160 " --> pdb=" O   SER D 137 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLY D 156 " --> pdb=" O   LEU D 141 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ASP D 161 " --> pdb=" O   TYR D 193 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   TYR D 193 " --> pdb=" O   ASP D 161 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   SER D 194 " --> pdb=" O   VAL D 186 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 170 through 171
      removed outlier: 3.810A  pdb=" N   ASN D 214 " --> pdb=" O   SER D 170 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   CYS D 213 " --> pdb=" O   LYS D 226 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LYS D 226 " --> pdb=" O   CYS D 213 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 232 through 241
      removed outlier: 6.152A  pdb=" N   LEU B 233 " --> pdb=" O   GLU B 252 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   GLU B 252 " --> pdb=" O   LEU B 233 " (cutoff:3.500A)
      removed outlier: 5.546A  pdb=" N   ASP B 235 " --> pdb=" O   HIS B 250 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   HIS B 250 " --> pdb=" O   ASP B 235 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   PHE B 249 " --> pdb=" O   ILE B 283 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 5 through 8
      removed outlier: 3.868A  pdb=" N   VAL E  20 " --> pdb=" O   ILE E  76 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ILE E  76 " --> pdb=" O   VAL E  20 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   THR E  73 " --> pdb=" O   SER E  66 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 11 through 13
      removed outlier: 3.982A  pdb=" N   GLU E 107 " --> pdb=" O   LEU E  12 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ILE E  49 " --> pdb=" O   TRP E  36 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   GLN E  38 " --> pdb=" O   LEU E  47 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   LEU E  47 " --> pdb=" O   GLN E  38 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 90 through 91
      removed outlier: 3.769A  pdb=" N   THR E  99 " --> pdb=" O   GLN E  91 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 116 through 119
      removed outlier: 3.861A  pdb=" N   ASN E 140 " --> pdb=" O   TYR E 175 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   TYR E 175 " --> pdb=" O   ASN E 140 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 6 through 10
      removed outlier: 3.602A  pdb=" N   VAL F   8 " --> pdb=" O   ALA F  26 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LEU F  23 " --> pdb=" O   LEU F  84 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   THR F  81 " --> pdb=" O   ASP F  76 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 48 through 53
      removed outlier: 7.073A  pdb=" N   TRP F  39 " --> pdb=" O   VAL F  51 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 106 through 107
    Processing sheet with id=AC4, first strand: chain 'F' and resid 137 through 141
      removed outlier: 3.540A  pdb=" N   LYS F 160 " --> pdb=" O   SER F 137 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLY F 156 " --> pdb=" O   LEU F 141 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'F' and resid 167 through 171
      removed outlier: 3.823A  pdb=" N   ASN F 214 " --> pdb=" O   SER F 170 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   CYS F 213 " --> pdb=" O   LYS F 226 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LYS F 226 " --> pdb=" O   CYS F 213 " (cutoff:3.500A)

    424 hydrogen bonds defined for protein.
    1170 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: 2.94

  Time building geometry restraints manager: 2.97 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3352
        1.34 -     1.46: 2439
        1.46 -     1.58: 4869
        1.58 -     1.69: 0
        1.69 -     1.81: 38
  Bond restraints: 10698
  Sorted by residual:
  bond pdb=" N   THR B 147 "
       pdb=" CA  THR B 147 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.017 1.29e-02 6.01e+03 1.65e+00
  bond pdb=" N   THR A 147 "
       pdb=" CA  THR A 147 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.015 1.29e-02 6.01e+03 1.35e+00
  bond pdb=" CG  PRO E  96 "
       pdb=" CD  PRO E  96 "
    ideal  model  delta    sigma   weight residual
    1.512  1.482  0.030 2.70e-02 1.37e+03 1.26e+00
  bond pdb=" CB  TRP D  50 "
       pdb=" CG  TRP D  50 "
    ideal  model  delta    sigma   weight residual
    1.498  1.466  0.032 3.10e-02 1.04e+03 1.04e+00
  bond pdb=" CB  TRP C  95 "
       pdb=" CG  TRP C  95 "
    ideal  model  delta    sigma   weight residual
    1.498  1.467  0.031 3.10e-02 1.04e+03 9.70e-01
  ... (remaining 10693 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 14165
        1.37 -     2.75: 292
        2.75 -     4.12: 77
        4.12 -     5.49: 23
        5.49 -     6.87: 5
  Bond angle restraints: 14562
  Sorted by residual:
  angle pdb=" C   GLN F 132 "
        pdb=" N   ILE F 133 "
        pdb=" CA  ILE F 133 "
      ideal   model   delta    sigma   weight residual
     121.97  128.84   -6.87 1.80e+00 3.09e-01 1.46e+01
  angle pdb=" C   GLN D 132 "
        pdb=" N   ILE D 133 "
        pdb=" CA  ILE D 133 "
      ideal   model   delta    sigma   weight residual
     121.97  127.64   -5.67 1.80e+00 3.09e-01 9.92e+00
  angle pdb=" C   PHE D 163 "
        pdb=" N   PRO D 164 "
        pdb=" CD  PRO D 164 "
      ideal   model   delta    sigma   weight residual
     120.60  126.49   -5.89 2.20e+00 2.07e-01 7.16e+00
  angle pdb=" C   PHE D 163 "
        pdb=" N   PRO D 164 "
        pdb=" CA  PRO D 164 "
      ideal   model   delta    sigma   weight residual
     127.00  120.72    6.28 2.40e+00 1.74e-01 6.85e+00
  angle pdb=" C   THR B 147 "
        pdb=" CA  THR B 147 "
        pdb=" CB  THR B 147 "
      ideal   model   delta    sigma   weight residual
     110.42  115.52   -5.10 1.99e+00 2.53e-01 6.57e+00
  ... (remaining 14557 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 5752
       17.84 -    35.67: 496
       35.67 -    53.51: 78
       53.51 -    71.35: 19
       71.35 -    89.19: 7
  Dihedral angle restraints: 6352
    sinusoidal: 2378
      harmonic: 3974
  Sorted by residual:
  dihedral pdb=" CB  CYS D  25 "
           pdb=" SG  CYS D  25 "
           pdb=" SG  CYS D  99 "
           pdb=" CB  CYS D  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  170.21  -77.21     1      1.00e+01 1.00e-02 7.47e+01
  dihedral pdb=" CB  CYS F  25 "
           pdb=" SG  CYS F  25 "
           pdb=" SG  CYS F  99 "
           pdb=" CB  CYS F  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  149.33  -56.33     1      1.00e+01 1.00e-02 4.28e+01
  dihedral pdb=" CB  CYS E 136 "
           pdb=" SG  CYS E 136 "
           pdb=" SG  CYS E 196 "
           pdb=" CB  CYS E 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  148.60  -55.60     1      1.00e+01 1.00e-02 4.18e+01
  ... (remaining 6349 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 986
       0.027 -    0.055: 470
       0.055 -    0.082: 134
       0.082 -    0.109: 80
       0.109 -    0.137: 24
  Chirality restraints: 1694
  Sorted by residual:
  chirality pdb=" CA  ILE E  49 "
            pdb=" N   ILE E  49 "
            pdb=" C   ILE E  49 "
            pdb=" CB  ILE E  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.67e-01
  chirality pdb=" CA  ILE C  49 "
            pdb=" N   ILE C  49 "
            pdb=" C   ILE C  49 "
            pdb=" CB  ILE C  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.56e-01
  chirality pdb=" CA  VAL D  96 "
            pdb=" N   VAL D  96 "
            pdb=" C   VAL D  96 "
            pdb=" CB  VAL D  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.24e-01
  ... (remaining 1691 not shown)

  Planarity restraints: 1834
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE F 163 "    0.049 5.00e-02 4.00e+02   7.48e-02 8.94e+00
        pdb=" N   PRO F 164 "   -0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO F 164 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO F 164 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D 165 "    0.037 5.00e-02 4.00e+02   5.61e-02 5.04e+00
        pdb=" N   PRO D 166 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO D 166 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO D 166 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU F 165 "   -0.031 5.00e-02 4.00e+02   4.64e-02 3.45e+00
        pdb=" N   PRO F 166 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO F 166 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO F 166 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1831 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 111
        2.63 -     3.20: 9498
        3.20 -     3.76: 15343
        3.76 -     4.33: 20423
        4.33 -     4.90: 34211
  Nonbonded interactions: 79586
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 287 "
            pdb="ZN    ZN B 302 "
     model   vdw
     2.060 2.230
  nonbonded pdb=" OD1 ASP A 287 "
            pdb="ZN    ZN A 304 "
     model   vdw
     2.062 2.230
  nonbonded pdb=" OD1 ASP B 287 "
            pdb="ZN    ZN B 301 "
     model   vdw
     2.066 2.230
  nonbonded pdb=" OD2 ASP A 287 "
            pdb="ZN    ZN A 301 "
     model   vdw
     2.071 2.230
  nonbonded pdb=" OD1 ASP A 159 "
            pdb="ZN    ZN A 303 "
     model   vdw
     2.090 2.230
  ... (remaining 79581 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.280
  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:             0.000
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     28.110
  Find NCS groups from input model:        0.520
  Set up NCS constraints:                  0.050
  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:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
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      :  0.003   0.032  10698  Z= 0.184
  Angle     :  0.546   6.869  14562  Z= 0.278
  Chirality :  0.039   0.137   1694
  Planarity :  0.004   0.075   1834
  Dihedral  : 13.515  89.186   3774
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  5.44 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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: -0.77 (0.24), residues: 1342
  helix:  0.28 (0.27), residues: 364
  sheet: -0.84 (0.30), residues: 342
  loop : -0.67 (0.26), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 179 
 HIS   0.002   0.001   HIS C 200 
 PHE   0.010   0.001   PHE D 183 
 TYR   0.012   0.001   TYR A 201 
 ARG   0.004   0.000   ARG C 144 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  139 PHE cc_start: 0.6512 (m-80) cc_final: 0.6287 (m-10)
REVERT: F  223 LYS cc_start: 0.8204 (mppt) cc_final: 0.7926 (mppt)
  outliers start: 0
  outliers final: 0
  residues processed: 236
  average time/residue: 0.2231
  time to fit residues: 74.1845
Evaluate side-chains
  203 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 113 optimal weight:    0.8980
   chunk 101 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 105 optimal weight:    1.9990
   chunk 40 optimal weight:    0.2980
   chunk 63 optimal weight:    0.9990
   chunk 78 optimal weight:   10.0000
   chunk 121 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A 285 HIS
D  38 HIS
D 102 GLN
B 285 HIS
E  91 GLN
E 140 ASN
** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.191208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.181411 restraints weight = 12527.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.180265 restraints weight = 23206.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.177689 restraints weight = 21385.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6926
moved from start:          0.1825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10698  Z= 0.258
  Angle     :  0.640   9.280  14562  Z= 0.325
  Chirality :  0.043   0.164   1694
  Planarity :  0.004   0.059   1834
  Dihedral  :  4.275  15.964   1466
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.41 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 10.21 %
    Favored  : 88.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.23), residues: 1342
  helix:  0.32 (0.26), residues: 400
  sheet: -1.06 (0.28), residues: 350
  loop : -0.87 (0.27), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP F 171 
 HIS   0.002   0.001   HIS B 250 
 PHE   0.025   0.002   PHE C 141 
 TYR   0.031   0.001   TYR E 142 
 ARG   0.005   0.000   ARG A 272 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 233
  time to evaluate  : 1.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   91 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8068 (pp30)
REVERT: E  139 ASN cc_start: 0.7822 (t0) cc_final: 0.7577 (t0)
  outliers start: 13
  outliers final: 10
  residues processed: 241
  average time/residue: 0.2324
  time to fit residues: 78.1100
Evaluate side-chains
  220 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 209
  time to evaluate  : 1.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  168 THR
Chi-restraints excluded: chain D residue  170 SER
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain E residue   91 GLN
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue  167 VAL
Chi-restraints excluded: chain F residue  186 VAL
Chi-restraints excluded: chain F residue  196 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 69 optimal weight:    9.9990
   chunk 52 optimal weight:    0.0670
   chunk 2 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 46 optimal weight:   10.0000
   chunk 105 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0070
   chunk 120 optimal weight:    0.7980
   chunk 133 optimal weight:    0.0270
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.3194

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

Flipped N/Q/H residues before XYZ refinement:
D 132 GLN
B 163 ASN
E  90 GLN
E  91 GLN
** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.193834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.177257 restraints weight = 12667.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.173704 restraints weight = 20421.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.172911 restraints weight = 24191.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6995
moved from start:          0.2301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10698  Z= 0.173
  Angle     :  0.608  11.680  14562  Z= 0.303
  Chirality :  0.042   0.164   1694
  Planarity :  0.004   0.055   1834
  Dihedral  :  4.068  14.466   1466
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.99 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 13.79 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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: -0.89 (0.23), residues: 1342
  helix:  0.40 (0.26), residues: 400
  sheet: -1.03 (0.28), residues: 340
  loop : -0.88 (0.26), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 179 
 HIS   0.002   0.001   HIS F 217 
 PHE   0.035   0.002   PHE B 184 
 TYR   0.026   0.001   TYR E 142 
 ARG   0.005   0.000   ARG C 144 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 230
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  139 ASN cc_start: 0.7587 (t0) cc_final: 0.7341 (t0)
REVERT: E   91 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7618 (pp30)
REVERT: E  139 ASN cc_start: 0.7694 (t0) cc_final: 0.7363 (t0)
  outliers start: 14
  outliers final: 7
  residues processed: 237
  average time/residue: 0.2196
  time to fit residues: 73.8217
Evaluate side-chains
  210 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 202
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  170 SER
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain E residue   91 GLN
Chi-restraints excluded: chain F residue  167 VAL
Chi-restraints excluded: chain F residue  196 SER
Chi-restraints excluded: chain F residue  213 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 63 optimal weight:    9.9990
   chunk 16 optimal weight:    6.9990
   chunk 43 optimal weight:    6.9990
   chunk 45 optimal weight:    9.9990
   chunk 87 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 129 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
C  38 GLN
D  42 GLN
E  91 GLN
** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  42 GLN
F 132 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.187182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.176218 restraints weight = 12528.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.174652 restraints weight = 27256.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.173225 restraints weight = 28868.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7033
moved from start:          0.2709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.093  10698  Z= 0.479
  Angle     :  0.717   9.532  14562  Z= 0.368
  Chirality :  0.046   0.166   1694
  Planarity :  0.005   0.050   1834
  Dihedral  :  4.729  19.552   1466
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  7.15 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 17.45 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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: -1.25 (0.23), residues: 1342
  helix:  0.30 (0.26), residues: 400
  sheet: -1.48 (0.26), residues: 386
  loop : -1.00 (0.27), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP D  50 
 HIS   0.005   0.001   HIS A 234 
 PHE   0.025   0.002   PHE E 141 
 TYR   0.028   0.002   TYR E 142 
 ARG   0.005   0.001   ARG A 272 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 222
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
REVERT: C   71 ASP cc_start: 0.7520 (m-30) cc_final: 0.7309 (m-30)
REVERT: C   91 GLN cc_start: 0.8439 (pp30) cc_final: 0.7834 (pp30)
REVERT: C  139 ASN cc_start: 0.7679 (t0) cc_final: 0.7342 (t0)
REVERT: E   91 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8041 (pp30)
REVERT: E  139 ASN cc_start: 0.7890 (t0) cc_final: 0.7527 (t0)
REVERT: F  133 ILE cc_start: 0.8063 (mp) cc_final: 0.7857 (mt)
  outliers start: 24
  outliers final: 17
  residues processed: 237
  average time/residue: 0.2441
  time to fit residues: 80.7274
Evaluate side-chains
  218 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 200
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  168 THR
Chi-restraints excluded: chain D residue  170 SER
Chi-restraints excluded: chain D residue  212 ILE
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain E residue   91 GLN
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue  138 VAL
Chi-restraints excluded: chain F residue  167 VAL
Chi-restraints excluded: chain F residue  196 SER
Chi-restraints excluded: chain F residue  198 VAL
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  213 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 114 optimal weight:    3.9990
   chunk 82 optimal weight:   10.0000
   chunk 127 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 106 optimal weight:    9.9990
   chunk 52 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   chunk 77 optimal weight:    0.1980
   chunk 97 optimal weight:    0.8980
   chunk 130 optimal weight:    0.0070
   overall best weight:    0.5800

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

Flipped N/Q/H residues before XYZ refinement:
D 112 HIS
B 248 GLN
E  91 GLN
** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 112 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.191351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.178978 restraints weight = 12474.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.178096 restraints weight = 22426.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.177374 restraints weight = 24596.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.4027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6941
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10698  Z= 0.222
  Angle     :  0.654  13.633  14562  Z= 0.323
  Chirality :  0.043   0.159   1694
  Planarity :  0.004   0.051   1834
  Dihedral  :  4.373  17.123   1466
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  5.51 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 18.50 %
    Favored  : 78.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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: -1.09 (0.23), residues: 1342
  helix:  0.40 (0.26), residues: 396
  sheet: -1.32 (0.26), residues: 368
  loop : -0.96 (0.27), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 179 
 HIS   0.002   0.000   HIS B 263 
 PHE   0.040   0.002   PHE B 184 
 TYR   0.039   0.001   TYR E 142 
 ARG   0.007   0.000   ARG B 202 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 216
  time to evaluate  : 1.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 GLU cc_start: 0.6467 (mt-10) cc_final: 0.6165 (mt-10)
REVERT: C   71 ASP cc_start: 0.7521 (m-30) cc_final: 0.7310 (m-30)
REVERT: C   91 GLN cc_start: 0.8441 (pp30) cc_final: 0.8074 (pp30)
REVERT: C  139 ASN cc_start: 0.7581 (t0) cc_final: 0.7195 (t0)
REVERT: D  168 THR cc_start: 0.6607 (OUTLIER) cc_final: 0.6370 (p)
REVERT: B   58 ASN cc_start: 0.6875 (t0) cc_final: 0.6604 (t0)
REVERT: B  278 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6625 (mm-30)
REVERT: E   91 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8060 (pp30)
REVERT: E  139 ASN cc_start: 0.7643 (t0) cc_final: 0.7292 (t0)
  outliers start: 29
  outliers final: 20
  residues processed: 233
  average time/residue: 0.2248
  time to fit residues: 73.6471
Evaluate side-chains
  220 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 198
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain C residue   95 TRP
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain D residue   86 MET
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain D residue  168 THR
Chi-restraints excluded: chain D residue  170 SER
Chi-restraints excluded: chain D residue  212 ILE
Chi-restraints excluded: chain D residue  215 VAL
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain E residue   91 GLN
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   37 ILE
Chi-restraints excluded: chain F residue  138 VAL
Chi-restraints excluded: chain F residue  167 VAL
Chi-restraints excluded: chain F residue  168 THR
Chi-restraints excluded: chain F residue  186 VAL
Chi-restraints excluded: chain F residue  196 SER
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  213 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 114 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 13 optimal weight:   40.0000
   chunk 61 optimal weight:    6.9990
   chunk 119 optimal weight:    0.0370
   chunk 62 optimal weight:    2.9990
   chunk 121 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 116 optimal weight:    0.8980
   chunk 131 optimal weight:    5.9990
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
D 132 GLN
** B  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  91 GLN
** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.191519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.182140 restraints weight = 12628.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.180555 restraints weight = 24489.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.177855 restraints weight = 23447.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6945
moved from start:          0.3001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10698  Z= 0.245
  Angle     :  0.675  10.882  14562  Z= 0.333
  Chirality :  0.043   0.158   1694
  Planarity :  0.004   0.050   1834
  Dihedral  :  4.344  17.071   1466
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  6.04 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 19.46 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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: -1.17 (0.23), residues: 1342
  helix:  0.33 (0.26), residues: 404
  sheet: -1.29 (0.27), residues: 354
  loop : -1.11 (0.26), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 179 
 HIS   0.004   0.001   HIS F 112 
 PHE   0.019   0.001   PHE E 141 
 TYR   0.033   0.001   TYR E 142 
 ARG   0.003   0.000   ARG B 202 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 210
  time to evaluate  : 1.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 GLU cc_start: 0.6527 (mt-10) cc_final: 0.6211 (mt-10)
REVERT: C   91 GLN cc_start: 0.8393 (pp30) cc_final: 0.7922 (pp30)
REVERT: C  139 ASN cc_start: 0.7502 (t0) cc_final: 0.7163 (t0)
REVERT: D  104 TYR cc_start: 0.6548 (OUTLIER) cc_final: 0.6077 (m-10)
REVERT: D  168 THR cc_start: 0.6691 (OUTLIER) cc_final: 0.6412 (p)
REVERT: E   91 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7708 (pp30)
REVERT: E  139 ASN cc_start: 0.7641 (t0) cc_final: 0.7271 (t0)
  outliers start: 35
  outliers final: 24
  residues processed: 231
  average time/residue: 0.2490
  time to fit residues: 79.7337
Evaluate side-chains
  217 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 190
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain C residue   95 TRP
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain D residue   37 ILE
Chi-restraints excluded: chain D residue   86 MET
Chi-restraints excluded: chain D residue  104 TYR
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  134 LYS
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain D residue  168 THR
Chi-restraints excluded: chain D residue  170 SER
Chi-restraints excluded: chain D residue  212 ILE
Chi-restraints excluded: chain D residue  215 VAL
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain E residue   91 GLN
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   37 ILE
Chi-restraints excluded: chain F residue  138 VAL
Chi-restraints excluded: chain F residue  167 VAL
Chi-restraints excluded: chain F residue  168 THR
Chi-restraints excluded: chain F residue  186 VAL
Chi-restraints excluded: chain F residue  196 SER
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  212 ILE
Chi-restraints excluded: chain F residue  213 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 126 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 82 optimal weight:    7.9990
   chunk 57 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 92 optimal weight:    0.7980
   chunk 101 optimal weight:    0.6980
   chunk 80 optimal weight:   30.0000
   chunk 95 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
E  91 GLN
** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.190213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.179168 restraints weight = 12778.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.176427 restraints weight = 26149.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.174361 restraints weight = 27657.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  10698  Z= 0.281
  Angle     :  0.676  10.061  14562  Z= 0.337
  Chirality :  0.044   0.164   1694
  Planarity :  0.005   0.069   1834
  Dihedral  :  4.418  17.250   1466
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  6.11 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 19.90 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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: -1.20 (0.23), residues: 1342
  helix:  0.38 (0.26), residues: 398
  sheet: -1.30 (0.27), residues: 358
  loop : -1.17 (0.26), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D  50 
 HIS   0.003   0.001   HIS F 112 
 PHE   0.019   0.002   PHE E 141 
 TYR   0.016   0.001   TYR D 162 
 ARG   0.007   0.000   ARG B 202 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 207
  time to evaluate  : 1.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 GLU cc_start: 0.6576 (mt-10) cc_final: 0.6257 (mt-10)
REVERT: C   91 GLN cc_start: 0.8401 (pp30) cc_final: 0.7986 (pp30)
REVERT: C  139 ASN cc_start: 0.7508 (t0) cc_final: 0.7155 (t0)
REVERT: D   92 GLU cc_start: 0.7481 (tp30) cc_final: 0.7269 (tp30)
REVERT: D  104 TYR cc_start: 0.6448 (OUTLIER) cc_final: 0.6035 (m-10)
REVERT: E   82 GLU cc_start: 0.7085 (pm20) cc_final: 0.6854 (tm-30)
REVERT: E   91 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7982 (pp30)
REVERT: E  139 ASN cc_start: 0.7580 (t0) cc_final: 0.7322 (t0)
REVERT: F  104 TYR cc_start: 0.6514 (OUTLIER) cc_final: 0.6078 (m-10)
  outliers start: 38
  outliers final: 27
  residues processed: 231
  average time/residue: 0.2237
  time to fit residues: 73.1720
Evaluate side-chains
  231 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 201
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   95 TRP
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain D residue   37 ILE
Chi-restraints excluded: chain D residue   86 MET
Chi-restraints excluded: chain D residue  104 TYR
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  134 LYS
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain D residue  168 THR
Chi-restraints excluded: chain D residue  170 SER
Chi-restraints excluded: chain D residue  215 VAL
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain E residue   91 GLN
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain F residue   37 ILE
Chi-restraints excluded: chain F residue  104 TYR
Chi-restraints excluded: chain F residue  138 VAL
Chi-restraints excluded: chain F residue  167 VAL
Chi-restraints excluded: chain F residue  168 THR
Chi-restraints excluded: chain F residue  186 VAL
Chi-restraints excluded: chain F residue  196 SER
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  212 ILE
Chi-restraints excluded: chain F residue  213 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 36 optimal weight:    0.5980
   chunk 84 optimal weight:    8.9990
   chunk 9 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 124 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 110 optimal weight:    3.9990
   chunk 119 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  91 GLN
E 140 ASN
** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.188879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.177025 restraints weight = 12763.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.174590 restraints weight = 25709.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.173368 restraints weight = 28068.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7021
moved from start:          0.3264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  10698  Z= 0.334
  Angle     :  0.712   9.631  14562  Z= 0.356
  Chirality :  0.044   0.162   1694
  Planarity :  0.005   0.059   1834
  Dihedral  :  4.584  17.826   1466
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  6.33 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 20.51 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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: -1.27 (0.23), residues: 1342
  helix:  0.41 (0.27), residues: 398
  sheet: -1.43 (0.26), residues: 372
  loop : -1.20 (0.26), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D  50 
 HIS   0.003   0.001   HIS F 112 
 PHE   0.016   0.002   PHE E 141 
 TYR   0.020   0.002   TYR E  50 
 ARG   0.006   0.000   ARG C 144 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 212
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 GLU cc_start: 0.6580 (mt-10) cc_final: 0.6205 (mt-10)
REVERT: C   91 GLN cc_start: 0.8497 (pp30) cc_final: 0.7852 (pp30)
REVERT: C  139 ASN cc_start: 0.7518 (t0) cc_final: 0.7149 (t0)
REVERT: D   92 GLU cc_start: 0.7554 (tp30) cc_final: 0.7341 (tp30)
REVERT: D  104 TYR cc_start: 0.6480 (OUTLIER) cc_final: 0.6056 (m-10)
REVERT: D  123 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7665 (mm-40)
REVERT: E   82 GLU cc_start: 0.7124 (pm20) cc_final: 0.6896 (tm-30)
REVERT: E   91 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7784 (pp30)
REVERT: E  139 ASN cc_start: 0.7803 (t0) cc_final: 0.7470 (t0)
REVERT: F  104 TYR cc_start: 0.6474 (OUTLIER) cc_final: 0.6040 (m-10)
  outliers start: 34
  outliers final: 28
  residues processed: 230
  average time/residue: 0.2373
  time to fit residues: 75.8596
Evaluate side-chains
  234 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 203
  time to evaluate  : 1.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue   95 TRP
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain D residue   37 ILE
Chi-restraints excluded: chain D residue   86 MET
Chi-restraints excluded: chain D residue  104 TYR
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain D residue  168 THR
Chi-restraints excluded: chain D residue  170 SER
Chi-restraints excluded: chain D residue  215 VAL
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain E residue   91 GLN
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain F residue   33 TYR
Chi-restraints excluded: chain F residue   37 ILE
Chi-restraints excluded: chain F residue  104 TYR
Chi-restraints excluded: chain F residue  138 VAL
Chi-restraints excluded: chain F residue  167 VAL
Chi-restraints excluded: chain F residue  168 THR
Chi-restraints excluded: chain F residue  186 VAL
Chi-restraints excluded: chain F residue  196 SER
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  212 ILE
Chi-restraints excluded: chain F residue  213 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 98 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 120 optimal weight:    0.0470
   chunk 12 optimal weight:   10.0000
   chunk 78 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
B 163 ASN
E  91 GLN
** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.191388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.180702 restraints weight = 12881.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.180036 restraints weight = 24923.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.176916 restraints weight = 21175.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.4010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6963
moved from start:          0.3368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10698  Z= 0.243
  Angle     :  0.699  10.018  14562  Z= 0.347
  Chirality :  0.044   0.175   1694
  Planarity :  0.005   0.063   1834
  Dihedral  :  4.482  17.424   1466
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  6.04 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 20.86 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.23), residues: 1342
  helix:  0.47 (0.27), residues: 398
  sheet: -1.35 (0.27), residues: 358
  loop : -1.24 (0.26), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP F  50 
 HIS   0.002   0.001   HIS F 112 
 PHE   0.017   0.002   PHE E 141 
 TYR   0.025   0.001   TYR C 142 
 ARG   0.008   0.000   ARG C 144 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 205
  time to evaluate  : 1.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 GLU cc_start: 0.6590 (mt-10) cc_final: 0.6271 (mt-10)
REVERT: C   91 GLN cc_start: 0.8409 (pp30) cc_final: 0.7770 (pp30)
REVERT: C  139 ASN cc_start: 0.7382 (t0) cc_final: 0.7002 (t0)
REVERT: D  104 TYR cc_start: 0.6381 (OUTLIER) cc_final: 0.5961 (m-10)
REVERT: D  111 ARG cc_start: 0.7382 (mmp-170) cc_final: 0.7088 (mmp-170)
REVERT: D  123 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7672 (mm-40)
REVERT: E   91 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7675 (pp30)
REVERT: F  104 TYR cc_start: 0.6381 (OUTLIER) cc_final: 0.5860 (m-10)
  outliers start: 34
  outliers final: 26
  residues processed: 223
  average time/residue: 0.2248
  time to fit residues: 71.1247
Evaluate side-chains
  224 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 195
  time to evaluate  : 1.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue   95 TRP
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain D residue   37 ILE
Chi-restraints excluded: chain D residue   86 MET
Chi-restraints excluded: chain D residue  104 TYR
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain D residue  168 THR
Chi-restraints excluded: chain D residue  170 SER
Chi-restraints excluded: chain D residue  215 VAL
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain E residue   91 GLN
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain F residue   33 TYR
Chi-restraints excluded: chain F residue   37 ILE
Chi-restraints excluded: chain F residue  104 TYR
Chi-restraints excluded: chain F residue  138 VAL
Chi-restraints excluded: chain F residue  167 VAL
Chi-restraints excluded: chain F residue  168 THR
Chi-restraints excluded: chain F residue  186 VAL
Chi-restraints excluded: chain F residue  196 SER
Chi-restraints excluded: chain F residue  212 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0980
   chunk 128 optimal weight:    5.9990
   chunk 69 optimal weight:   10.0000
   chunk 124 optimal weight:    3.9990
   chunk 130 optimal weight:    8.9990
   chunk 98 optimal weight:    0.9990
   chunk 77 optimal weight:   20.0000
   chunk 108 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 117 optimal weight:    1.9990
   overall best weight:    1.4188

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

Flipped N/Q/H residues before XYZ refinement:
D 102 GLN
E  91 GLN
** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.188005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.178732 restraints weight = 12720.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.163338 restraints weight = 24918.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.154876 restraints weight = 18485.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.3446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.082  10698  Z= 0.406
  Angle     :  0.780  15.022  14562  Z= 0.389
  Chirality :  0.046   0.183   1694
  Planarity :  0.005   0.075   1834
  Dihedral  :  4.766  18.636   1466
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  7.60 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 21.73 %
    Favored  : 75.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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: -1.36 (0.23), residues: 1342
  helix:  0.40 (0.27), residues: 398
  sheet: -1.50 (0.26), residues: 374
  loop : -1.30 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D  50 
 HIS   0.004   0.001   HIS F 112 
 PHE   0.016   0.002   PHE E  84 
 TYR   0.025   0.002   TYR E  50 
 ARG   0.011   0.001   ARG C 144 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 210
  time to evaluate  : 1.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6654 (mt-10)
REVERT: C   91 GLN cc_start: 0.8523 (pp30) cc_final: 0.8126 (pp30)
REVERT: C  139 ASN cc_start: 0.8003 (t0) cc_final: 0.7502 (t0)
REVERT: D  104 TYR cc_start: 0.6595 (OUTLIER) cc_final: 0.6157 (m-10)
REVERT: D  111 ARG cc_start: 0.7459 (mmp-170) cc_final: 0.6942 (mmp-170)
REVERT: D  123 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7873 (mm-40)
REVERT: B   93 MET cc_start: 0.8120 (mtp) cc_final: 0.7832 (ttm)
REVERT: E   82 GLU cc_start: 0.7600 (pm20) cc_final: 0.7132 (tm-30)
REVERT: E   91 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8248 (pp30)
REVERT: F  104 TYR cc_start: 0.6620 (OUTLIER) cc_final: 0.6207 (m-10)
  outliers start: 32
  outliers final: 25
  residues processed: 228
  average time/residue: 0.2204
  time to fit residues: 71.1841
Evaluate side-chains
  234 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 206
  time to evaluate  : 1.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain D residue   37 ILE
Chi-restraints excluded: chain D residue   86 MET
Chi-restraints excluded: chain D residue  102 GLN
Chi-restraints excluded: chain D residue  104 TYR
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain D residue  168 THR
Chi-restraints excluded: chain D residue  170 SER
Chi-restraints excluded: chain D residue  215 VAL
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain E residue   91 GLN
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain F residue   33 TYR
Chi-restraints excluded: chain F residue   37 ILE
Chi-restraints excluded: chain F residue  104 TYR
Chi-restraints excluded: chain F residue  138 VAL
Chi-restraints excluded: chain F residue  167 VAL
Chi-restraints excluded: chain F residue  168 THR
Chi-restraints excluded: chain F residue  186 VAL
Chi-restraints excluded: chain F residue  196 SER
Chi-restraints excluded: chain F residue  212 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 107 optimal weight:    7.9990
   chunk 70 optimal weight:    0.3980
   chunk 93 optimal weight:    0.0570
   chunk 128 optimal weight:    4.9990
   chunk 131 optimal weight:    0.0670
   chunk 121 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 9 optimal weight:    8.9990
   chunk 41 optimal weight:    4.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    0.7040

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
E  91 GLN
** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 132 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.190354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.180044 restraints weight = 12582.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.179251 restraints weight = 23447.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.177719 restraints weight = 20870.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6944
moved from start:          0.3539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10698  Z= 0.256
  Angle     :  0.734  14.256  14562  Z= 0.363
  Chirality :  0.044   0.182   1694
  Planarity :  0.005   0.062   1834
  Dihedral  :  4.634  17.807   1466
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  6.04 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 22.08 %
    Favored  : 75.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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: -1.27 (0.23), residues: 1342
  helix:  0.49 (0.27), residues: 394
  sheet: -1.39 (0.27), residues: 358
  loop : -1.30 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP F  50 
 HIS   0.002   0.001   HIS F 112 
 PHE   0.014   0.002   PHE B  97 
 TYR   0.015   0.001   TYR E  50 
 ARG   0.010   0.000   ARG C 144 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3058.82 seconds
wall clock time: 56 minutes 13.32 seconds (3373.32 seconds total)