Starting phenix.real_space_refine
on Tue Nov 18 06:45:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6cmo_7517/11_2025/6cmo_7517.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6cmo_7517/11_2025/6cmo_7517.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6cmo_7517/11_2025/6cmo_7517.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6cmo_7517/11_2025/6cmo_7517.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6cmo_7517/11_2025/6cmo_7517.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6cmo_7517/11_2025/6cmo_7517.cif"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      83      5.16       5
     C    7519      2.51       5
     N    1979      2.21       5
     O    2253      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11834
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "R"
      Number of atoms: 2567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 2567
          Classifications: {'peptide': 323}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 304}
    Chain: "A"
      Number of atoms: 2834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 354, 2834
          Classifications: {'peptide': 354}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 349}
    Chain: "B"
      Number of atoms: 2616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2616
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "L"
      Number of atoms: 1602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1602
          Classifications: {'peptide': 211}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200}
    Chain: "H"
      Number of atoms: 1743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1743
          Classifications: {'peptide': 230}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 216}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 2.94, per 1000 atoms: 0.25
  Number of scatterers: 11834
  At special positions: 0
  Unit cell: (99.008, 152.32, 167.552, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      83     16.00
     O    2253      8.00
     N    1979      7.00
     C    7519      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS R   2 " - pdb=" SG  CYS R 282 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 110 " - pdb=" SG  CYS R 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 135 " - pdb=" SG  CYS L 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 158 " - pdb=" SG  CYS H 214 " 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
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG C   1 " - " ASN R  15 "
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 541.7 milliseconds
  

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2840

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 19 sheets defined
      37.1% alpha, 18.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'R' and resid 33 through 65
      removed outlier: 3.663A  pdb=" N   PHE R  37 " --> pdb=" O   GLU R  33 " (cutoff:3.500A)
      Proline residue:  R  53  - end of helix
    Processing helix  chain 'R' and resid 66 through 69
      removed outlier: 3.650A  pdb=" N   ARG R  69 " --> pdb=" O   LYS R  66 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 66 through 69'
    Processing helix  chain 'R' and resid 70 through 101
      removed outlier: 3.929A  pdb=" N   ILE R  75 " --> pdb=" O   PRO R  71 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLY R 101 " --> pdb=" O   THR R  97 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 106 through 141
      removed outlier: 3.684A  pdb=" N   CYS R 110 " --> pdb=" O   GLY R 106 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LYS R 141 " --> pdb=" O   VAL R 137 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 149 through 173
      removed outlier: 4.130A  pdb=" N   ALA R 153 " --> pdb=" O   GLY R 149 " (cutoff:3.500A)
      Proline residue:  R 170  - end of helix
    Processing helix  chain 'R' and resid 200 through 238
      Proline residue:  R 215  - end of helix
    Processing helix  chain 'R' and resid 240 through 278
      removed outlier: 3.904A  pdb=" N   GLN R 244 " --> pdb=" O   SER R 240 " (cutoff:3.500A)
      Proline residue:  R 267  - end of helix
    Processing helix  chain 'R' and resid 289 through 308
      removed outlier: 3.987A  pdb=" N   PHE R 293 " --> pdb=" O   THR R 289 " (cutoff:3.500A)
      Proline residue:  R 303  - end of helix
    Processing helix  chain 'R' and resid 310 through 323
    Processing helix  chain 'A' and resid 2 through 32
    Processing helix  chain 'A' and resid 42 through 53
    Processing helix  chain 'A' and resid 62 through 90
    Processing helix  chain 'A' and resid 100 through 113
      removed outlier: 3.599A  pdb=" N   ALA A 104 " --> pdb=" O   ARG A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.560A  pdb=" N   ALA A 124 " --> pdb=" O   THR A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 143
      removed outlier: 3.938A  pdb=" N   GLN A 137 " --> pdb=" O   ASP A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 146
      No H-bonds generated for 'chain 'A' and resid 144 through 146'
    Processing helix  chain 'A' and resid 151 through 163
    Processing helix  chain 'A' and resid 170 through 178
      removed outlier: 4.185A  pdb=" N   VAL A 174 " --> pdb=" O   THR A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 214
    Processing helix  chain 'A' and resid 226 through 231
      removed outlier: 4.036A  pdb=" N   TYR A 230 " --> pdb=" O   LEU A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 4.266A  pdb=" N   GLU A 245 " --> pdb=" O   ASN A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.608A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 281
    Processing helix  chain 'A' and resid 289 through 293
      removed outlier: 4.489A  pdb=" N   SER A 293 " --> pdb=" O   TYR A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 310
      removed outlier: 3.585A  pdb=" N   TYR A 302 " --> pdb=" O   GLU A 298 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ILE A 303 " --> pdb=" O   ALA A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 351
      removed outlier: 3.907A  pdb=" N   ASN A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLN A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   PHE A 334 " --> pdb=" O   LYS A 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 25
    Processing helix  chain 'B' and resid 29 through 36
      removed outlier: 4.221A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 24
      removed outlier: 3.984A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 47
    Processing helix  chain 'L' and resid 122 through 129
      removed outlier: 3.604A  pdb=" N   LEU L 126 " --> pdb=" O   SER L 122 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 184 through 189
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 4.092A  pdb=" N   THR H  94 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 172 through 176
      removed outlier: 3.663A  pdb=" N   GLY H 175 " --> pdb=" O   TRP H 172 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ALA H 176 " --> pdb=" O   ASN H 173 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 172 through 176'
    Processing helix  chain 'H' and resid 203 through 208
      removed outlier: 3.852A  pdb=" N   LEU H 207 " --> pdb=" O   SER H 204 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   GLY H 208 " --> pdb=" O   SER H 205 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 179 through 181
      removed outlier: 3.969A  pdb=" N   ILE R 179 " --> pdb=" O   GLY R 188 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   SER R 186 " --> pdb=" O   GLU R 181 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 191
      removed outlier: 3.559A  pdb=" N   THR A 187 " --> pdb=" O   MET A 198 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LEU A 194 " --> pdb=" O   PHE A 191 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   PHE A 199 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ILE A 221 " --> pdb=" O   SER A 263 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.022A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.757A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.823A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   SER B  72 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ILE B  80 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 5.654A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.001A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.588A  pdb=" N   THR B 102 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ALA B 113 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ILE B 123 " --> pdb=" O   ARG B 137 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151
      removed outlier: 3.675A  pdb=" N   VAL B 158 " --> pdb=" O   ARG B 150 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.259A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   GLY B 202 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   SER B 191 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 232 through 234
      removed outlier: 3.590A  pdb=" N   CYS B 233 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU B 252 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.675A  pdb=" N   ALA B 287 " --> pdb=" O   ASN B 295 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ASN B 295 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 20 through 25
      removed outlier: 3.552A  pdb=" N   VAL L  20 " --> pdb=" O   ILE L  76 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ILE L  76 " --> pdb=" O   VAL L  20 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   THR L  73 " --> pdb=" O   SER L  66 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   THR L  75 " --> pdb=" O   SER L  64 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 54 through 55
      removed outlier: 6.812A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 115 through 118
      removed outlier: 4.856A  pdb=" N   CYS L 135 " --> pdb=" O   SER L 178 " (cutoff:3.500A)
      removed outlier: 5.655A  pdb=" N   SER L 178 " --> pdb=" O   CYS L 135 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   LEU L 137 " --> pdb=" O   LEU L 176 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   LEU L 176 " --> pdb=" O   LEU L 137 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   TYR L 174 " --> pdb=" O   ASN L 139 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 130 through 131
      removed outlier: 4.053A  pdb=" N   ALA L 131 " --> pdb=" O   LEU L 182 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   LEU L 182 " --> pdb=" O   ALA L 131 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'L' and resid 149 through 151
      removed outlier: 4.056A  pdb=" N   LYS L 150 " --> pdb=" O   ALA L 194 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   ALA L 194 " --> pdb=" O   LYS L 150 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'H' and resid 6 through 10
      removed outlier: 4.125A  pdb=" N   GLN H   6 " --> pdb=" O   SER H  28 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   SER H  28 " --> pdb=" O   GLN H   6 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL H   8 " --> pdb=" O   ALA H  26 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   LEU H  21 " --> pdb=" O   MET H  86 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   THR H  81 " --> pdb=" O   ASP H  76 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   SER H  74 " --> pdb=" O   TYR H  83 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   THR H  72 " --> pdb=" O   GLN H  85 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 13 through 15
      removed outlier: 4.119A  pdb=" N   GLY H  13 " --> pdb=" O   LEU H 126 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   THR H 128 " --> pdb=" O   GLY H  13 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR H 125 " --> pdb=" O   TYR H  97 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   TYR H  98 " --> pdb=" O   VAL H  40 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   VAL H  40 " --> pdb=" O   TYR H  98 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 13 through 15
      removed outlier: 4.119A  pdb=" N   GLY H  13 " --> pdb=" O   LEU H 126 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   THR H 128 " --> pdb=" O   GLY H  13 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR H 125 " --> pdb=" O   TYR H  97 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   TYR H 120 " --> pdb=" O   ARG H 101 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'H' and resid 138 through 141
      removed outlier: 4.267A  pdb=" N   CYS H 158 " --> pdb=" O   SER H 198 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   SER H 198 " --> pdb=" O   CYS H 158 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   TYR H 194 " --> pdb=" O   ASP H 162 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   SER H 195 " --> pdb=" O   ALA H 186 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   ALA H 186 " --> pdb=" O   SER H 195 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   SER H 197 " --> pdb=" O   PHE H 184 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'H' and resid 214 through 218
      removed outlier: 4.512A  pdb=" N   CYS H 214 " --> pdb=" O   LYS H 227 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   LYS H 227 " --> pdb=" O   CYS H 214 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   VAL H 216 " --> pdb=" O   VAL H 225 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL H 225 " --> pdb=" O   VAL H 216 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   HIS H 218 " --> pdb=" O   THR H 223 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   THR H 223 " --> pdb=" O   HIS H 218 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC1

    519 hydrogen bonds defined for protein.
    1488 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: 1.75

  Time building geometry restraints manager: 1.04 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3759
        1.34 -     1.46: 2865
        1.46 -     1.58: 5356
        1.58 -     1.70: 0
        1.70 -     1.82: 119
  Bond restraints: 12099
  Sorted by residual:
  bond pdb=" C   ASN R 302 "
       pdb=" N   PRO R 303 "
    ideal  model  delta    sigma   weight residual
    1.335  1.363 -0.027 1.36e-02 5.41e+03 4.08e+00
  bond pdb=" CB  PHE R  91 "
       pdb=" CG  PHE R  91 "
    ideal  model  delta    sigma   weight residual
    1.502  1.547 -0.045 2.30e-02 1.89e+03 3.78e+00
  bond pdb=" C   ILE R 214 "
       pdb=" N   PRO R 215 "
    ideal  model  delta    sigma   weight residual
    1.336  1.359 -0.023 1.23e-02 6.61e+03 3.53e+00
  bond pdb=" C   VAL R 266 "
       pdb=" N   PRO R 267 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.024 1.28e-02 6.10e+03 3.50e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.14e+00
  ... (remaining 12094 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.93: 16077
        2.93 -     5.87: 275
        5.87 -     8.80: 46
        8.80 -    11.73: 12
       11.73 -    14.66: 2
  Bond angle restraints: 16412
  Sorted by residual:
  angle pdb=" N   GLU A 297 "
        pdb=" CA  GLU A 297 "
        pdb=" C   GLU A 297 "
      ideal   model   delta    sigma   weight residual
     111.11  118.12   -7.01 1.20e+00 6.94e-01 3.42e+01
  angle pdb=" CA  TYR R  43 "
        pdb=" CB  TYR R  43 "
        pdb=" CG  TYR R  43 "
      ideal   model   delta    sigma   weight residual
     113.90  123.74   -9.84 1.80e+00 3.09e-01 2.99e+01
  angle pdb=" C   THR A 327 "
        pdb=" N   ASP A 328 "
        pdb=" CA  ASP A 328 "
      ideal   model   delta    sigma   weight residual
     120.38  127.74   -7.36 1.46e+00 4.69e-01 2.54e+01
  angle pdb=" N   ILE R 290 "
        pdb=" CA  ILE R 290 "
        pdb=" C   ILE R 290 "
      ideal   model   delta    sigma   weight residual
     108.88  118.21   -9.33 2.16e+00 2.14e-01 1.87e+01
  angle pdb=" C   ALA A 203 "
        pdb=" N   GLN A 204 "
        pdb=" CA  GLN A 204 "
      ideal   model   delta    sigma   weight residual
     120.63  127.57   -6.94 1.61e+00 3.86e-01 1.86e+01
  ... (remaining 16407 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.99: 6774
       14.99 -    29.97: 343
       29.97 -    44.96: 92
       44.96 -    59.95: 11
       59.95 -    74.93: 7
  Dihedral angle restraints: 7227
    sinusoidal: 2810
      harmonic: 4417
  Sorted by residual:
  dihedral pdb=" CA  CYS R 110 "
           pdb=" C   CYS R 110 "
           pdb=" N   ASN R 111 "
           pdb=" CA  ASN R 111 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.69   23.31     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CA  SER A 151 "
           pdb=" C   SER A 151 "
           pdb=" N   ALA A 152 "
           pdb=" CA  ALA A 152 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.08  -21.92     0      5.00e+00 4.00e-02 1.92e+01
  dihedral pdb=" CA  ASN A 149 "
           pdb=" C   ASN A 149 "
           pdb=" N   ASP A 150 "
           pdb=" CA  ASP A 150 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.21  -20.79     0      5.00e+00 4.00e-02 1.73e+01
  ... (remaining 7224 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.206: 1834
       0.206 -    0.411: 9
       0.411 -    0.617: 0
       0.617 -    0.823: 0
       0.823 -    1.029: 1
  Chirality restraints: 1844
  Sorted by residual:
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN R  15 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.37   -1.03 2.00e-01 2.50e+01 2.65e+01
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.34   -0.06 2.00e-02 2.50e+03 1.01e+01
  chirality pdb=" CB  ILE R 123 "
            pdb=" CA  ILE R 123 "
            pdb=" CG1 ILE R 123 "
            pdb=" CG2 ILE R 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.30 2.00e-01 2.50e+01 2.21e+00
  ... (remaining 1841 not shown)

  Planarity restraints: 2090
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN R  15 "    0.195 2.00e-02 2.50e+03   2.09e-01 5.46e+02
        pdb=" CG  ASN R  15 "   -0.092 2.00e-02 2.50e+03
        pdb=" OD1 ASN R  15 "   -0.051 2.00e-02 2.50e+03
        pdb=" ND2 ASN R  15 "   -0.316 2.00e-02 2.50e+03
        pdb=" C1  NAG C   1 "    0.264 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R  35 "    0.022 2.00e-02 2.50e+03   1.74e-02 7.56e+00
        pdb=" CG  TRP R  35 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP R  35 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP R  35 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP R  35 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP R  35 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP R  35 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R  35 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R  35 "    0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP R  35 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "    0.042 5.00e-02 4.00e+02   6.38e-02 6.50e+00
        pdb=" N   PRO G  49 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "    0.035 5.00e-02 4.00e+02
  ... (remaining 2087 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 453
        2.72 -     3.27: 11087
        3.27 -     3.81: 17965
        3.81 -     4.36: 20784
        4.36 -     4.90: 35731
  Nonbonded interactions: 86020
  Sorted by model distance:
  nonbonded pdb=" O   LEU R  88 "
            pdb=" OG1 THR R  92 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" O   ASP A 173 "
            pdb=" OG1 THR A 177 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   SER A  44 "
            pdb=" OG1 THR A  48 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   LYS A 248 "
            pdb=" OG  SER A 252 "
     model   vdw
     2.322 3.040
  ... (remaining 86015 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.170
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6842
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      :  0.004   0.069  12107  Z= 0.223
  Angle     :  1.011  18.756  16430  Z= 0.537
  Chirality :  0.063   1.029   1844
  Planarity :  0.007   0.064   2089
  Dihedral  : 10.429  74.935   4369
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  4.34 %
    Favored  : 95.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.97 (0.18), residues: 1504
  helix: -1.67 (0.19), residues: 507
  sheet:  0.09 (0.28), residues: 255
  loop : -1.49 (0.18), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R  69 
 TYR   0.022   0.002   TYR A 296 
 PHE   0.033   0.003   PHE R  37 
 TRP   0.046   0.003   TRP R  35 
 HIS   0.009   0.002   HIS R 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (12099)
  covalent geometry    : angle       0.99534 (16412)
  SS BOND              : bond        0.00235 (    6)
  SS BOND              : angle       2.13738 (   12)
  hydrogen bonds       : bond        0.18521 (  515)
  hydrogen bonds       : angle       9.45612 ( 1488)
  link_BETA1-4         : bond        0.00611 (    1)
  link_BETA1-4         : angle       1.95576 (    3)
  link_NAG-ASN         : bond        0.03150 (    1)
  link_NAG-ASN         : angle      12.68548 (    3)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 330
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  143 MET cc_start: 0.6283 (mtm) cc_final: 0.5672 (mtt)
REVERT: R  175 TRP cc_start: 0.3848 (t-100) cc_final: 0.3164 (t-100)
REVERT: R  225 GLN cc_start: 0.7327 (tp40) cc_final: 0.7032 (tp40)
REVERT: R  278 HIS cc_start: 0.5773 (m90) cc_final: 0.5418 (m90)
REVERT: A  107 LEU cc_start: 0.7557 (tt) cc_final: 0.6632 (mm)
REVERT: A  154 TYR cc_start: 0.7520 (t80) cc_final: 0.7297 (t80)
REVERT: A  195 HIS cc_start: 0.6407 (m-70) cc_final: 0.6161 (m90)
REVERT: A  234 LEU cc_start: 0.5271 (tp) cc_final: 0.4831 (tp)
REVERT: A  269 ASN cc_start: 0.7909 (m-40) cc_final: 0.7560 (p0)
REVERT: A  290 TYR cc_start: 0.4900 (t80) cc_final: 0.4207 (t80)
REVERT: A  347 ASN cc_start: 0.7609 (m110) cc_final: 0.7361 (m-40)
REVERT: B    9 GLN cc_start: 0.7029 (mp10) cc_final: 0.6698 (mp10)
REVERT: B   75 GLN cc_start: 0.7007 (mt0) cc_final: 0.6021 (tm-30)
REVERT: B   76 ASP cc_start: 0.6995 (p0) cc_final: 0.6290 (p0)
REVERT: B  120 ILE cc_start: 0.8531 (mt) cc_final: 0.8142 (mm)
REVERT: B  201 SER cc_start: 0.8353 (t) cc_final: 0.7962 (p)
REVERT: B  254 ASP cc_start: 0.7160 (t0) cc_final: 0.6894 (t70)
REVERT: B  264 TYR cc_start: 0.7183 (m-10) cc_final: 0.6897 (m-10)
REVERT: B  340 ASN cc_start: 0.6160 (t160) cc_final: 0.5916 (t0)
REVERT: G   38 MET cc_start: 0.7865 (ppp) cc_final: 0.6655 (tpt)
REVERT: L   64 SER cc_start: 0.7485 (m) cc_final: 0.7147 (p)
REVERT: L  166 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6563 (mt-10)
REVERT: H  105 TYR cc_start: 0.5377 (p90) cc_final: 0.4328 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 330
  average time/residue: 0.1271
  time to fit residues: 57.1080
Evaluate side-chains
  178 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 149 optimal weight:    7.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
R 111 ASN
** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 119 ASN
B 259 GLN
B 293 ASN
B 311 HIS
B 340 ASN
G  11 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 159 ASN
L 199 HIS
L 211 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.124959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.102575 restraints weight = 32360.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.101079 restraints weight = 35465.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.102342 restraints weight = 28642.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.102572 restraints weight = 20578.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.102655 restraints weight = 21523.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6846
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12107  Z= 0.217
  Angle     :  0.747  10.539  16430  Z= 0.398
  Chirality :  0.047   0.207   1844
  Planarity :  0.006   0.088   2089
  Dihedral  :  6.145  51.142   1685
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  4.81 %
    Favored  : 94.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.19), residues: 1504
  helix: -0.44 (0.21), residues: 528
  sheet: -0.07 (0.28), residues: 270
  loop : -1.39 (0.19), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG L 109 
 TYR   0.040   0.003   TYR A 290 
 PHE   0.027   0.003   PHE B 241 
 TRP   0.020   0.003   TRP R  35 
 HIS   0.009   0.002   HIS L 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (12099)
  covalent geometry    : angle       0.74461 (16412)
  SS BOND              : bond        0.00561 (    6)
  SS BOND              : angle       1.09434 (   12)
  hydrogen bonds       : bond        0.05577 (  515)
  hydrogen bonds       : angle       6.08886 ( 1488)
  link_BETA1-4         : bond        0.00200 (    1)
  link_BETA1-4         : angle       1.47247 (    3)
  link_NAG-ASN         : bond        0.00380 (    1)
  link_NAG-ASN         : angle       3.99646 (    3)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 218
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  175 TRP cc_start: 0.4622 (t-100) cc_final: 0.3838 (t-100)
REVERT: A   15 ARG cc_start: 0.6879 (mtm-85) cc_final: 0.5986 (ptm160)
REVERT: A  139 CYS cc_start: 0.7491 (m) cc_final: 0.7259 (m)
REVERT: A  302 TYR cc_start: 0.4543 (t80) cc_final: 0.3527 (t80)
REVERT: A  346 ASN cc_start: 0.7210 (t0) cc_final: 0.6936 (t0)
REVERT: B   75 GLN cc_start: 0.6976 (mt0) cc_final: 0.6352 (tm-30)
REVERT: B  254 ASP cc_start: 0.7284 (t0) cc_final: 0.6965 (t0)
REVERT: B  331 SER cc_start: 0.8967 (t) cc_final: 0.8544 (m)
REVERT: G   28 ILE cc_start: 0.8358 (mm) cc_final: 0.8015 (tt)
REVERT: G   38 MET cc_start: 0.6840 (ppp) cc_final: 0.6402 (tpt)
  outliers start: 6
  outliers final: 3
  residues processed: 222
  average time/residue: 0.1041
  time to fit residues: 33.2888
Evaluate side-chains
  153 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 150
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 37 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 129 optimal weight:    2.9990
   chunk 104 optimal weight:    4.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
R 111 ASN
** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 159 ASN
L 199 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.127073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.104718 restraints weight = 31827.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.103748 restraints weight = 28918.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.104681 restraints weight = 27193.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.105015 restraints weight = 20123.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.105248 restraints weight = 18929.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6799
moved from start:          0.3154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12107  Z= 0.138
  Angle     :  0.646   9.446  16430  Z= 0.340
  Chirality :  0.044   0.209   1844
  Planarity :  0.005   0.078   2089
  Dihedral  :  5.658  51.777   1685
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  4.19 %
    Favored  : 95.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.94 (0.20), residues: 1504
  helix: -0.00 (0.22), residues: 517
  sheet:  0.15 (0.30), residues: 267
  loop : -1.37 (0.20), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 176 
 TYR   0.020   0.002   TYR L 141 
 PHE   0.021   0.002   PHE R 221 
 TRP   0.016   0.001   TRP R  35 
 HIS   0.008   0.001   HIS L 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (12099)
  covalent geometry    : angle       0.64437 (16412)
  SS BOND              : bond        0.00480 (    6)
  SS BOND              : angle       0.92342 (   12)
  hydrogen bonds       : bond        0.04920 (  515)
  hydrogen bonds       : angle       5.47631 ( 1488)
  link_BETA1-4         : bond        0.00137 (    1)
  link_BETA1-4         : angle       1.25506 (    3)
  link_NAG-ASN         : bond        0.00207 (    1)
  link_NAG-ASN         : angle       3.31453 (    3)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 214
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   83 ASP cc_start: 0.7484 (t0) cc_final: 0.7235 (t0)
REVERT: R  175 TRP cc_start: 0.4872 (t-100) cc_final: 0.3945 (t-100)
REVERT: R  255 ILE cc_start: 0.7547 (pt) cc_final: 0.7268 (mm)
REVERT: R  257 TYR cc_start: 0.7463 (m-10) cc_final: 0.5893 (m-80)
REVERT: A   15 ARG cc_start: 0.7107 (mtm-85) cc_final: 0.6073 (ptm160)
REVERT: A   24 ARG cc_start: 0.6914 (mmp-170) cc_final: 0.6633 (mmp-170)
REVERT: A   74 TYR cc_start: 0.7172 (m-80) cc_final: 0.6890 (m-80)
REVERT: A  178 ARG cc_start: 0.6632 (tpt170) cc_final: 0.6230 (ptp-110)
REVERT: A  296 TYR cc_start: 0.5892 (p90) cc_final: 0.5654 (p90)
REVERT: B   75 GLN cc_start: 0.6689 (mt0) cc_final: 0.6007 (tm-30)
REVERT: B  186 ASP cc_start: 0.8295 (t0) cc_final: 0.7965 (t0)
REVERT: B  214 ARG cc_start: 0.8050 (mtm-85) cc_final: 0.7586 (mtm-85)
REVERT: B  228 ASP cc_start: 0.8045 (m-30) cc_final: 0.7735 (m-30)
REVERT: B  254 ASP cc_start: 0.7132 (t0) cc_final: 0.6711 (t0)
REVERT: B  331 SER cc_start: 0.8907 (t) cc_final: 0.8497 (m)
REVERT: G   28 ILE cc_start: 0.8390 (mm) cc_final: 0.7937 (tt)
REVERT: G   38 MET cc_start: 0.6743 (ppp) cc_final: 0.6501 (tpt)
REVERT: L  141 TYR cc_start: 0.5244 (m-10) cc_final: 0.4867 (m-80)
REVERT: H  105 TYR cc_start: 0.5695 (p90) cc_final: 0.5443 (p90)
REVERT: H  112 TYR cc_start: 0.6249 (m-10) cc_final: 0.5259 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 215
  average time/residue: 0.1067
  time to fit residues: 33.2643
Evaluate side-chains
  161 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 106 optimal weight:   10.0000
   chunk 64 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 75 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 124 optimal weight:    9.9990
   chunk 41 optimal weight:    0.0370
   overall best weight:    1.1864

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

Flipped N/Q/H residues before XYZ refinement:
R  78 ASN
** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
B 340 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 159 ASN
L 199 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.126275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.104606 restraints weight = 32022.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.102500 restraints weight = 36512.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.103384 restraints weight = 32379.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.104986 restraints weight = 24151.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.105035 restraints weight = 19201.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6810
moved from start:          0.3554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  12107  Z= 0.135
  Angle     :  0.632  10.906  16430  Z= 0.333
  Chirality :  0.044   0.193   1844
  Planarity :  0.005   0.057   2089
  Dihedral  :  5.614  59.801   1685
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  4.42 %
    Favored  : 95.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.20), residues: 1504
  helix:  0.16 (0.22), residues: 511
  sheet:  0.04 (0.30), residues: 277
  loop : -1.30 (0.20), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  62 
 TYR   0.033   0.002   TYR A  69 
 PHE   0.023   0.002   PHE R 221 
 TRP   0.034   0.002   TRP R  35 
 HIS   0.008   0.001   HIS L 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (12099)
  covalent geometry    : angle       0.63078 (16412)
  SS BOND              : bond        0.00397 (    6)
  SS BOND              : angle       0.90621 (   12)
  hydrogen bonds       : bond        0.04703 (  515)
  hydrogen bonds       : angle       5.28358 ( 1488)
  link_BETA1-4         : bond        0.00071 (    1)
  link_BETA1-4         : angle       1.59402 (    3)
  link_NAG-ASN         : bond        0.00212 (    1)
  link_NAG-ASN         : angle       2.56278 (    3)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 216
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   83 ASP cc_start: 0.7471 (t0) cc_final: 0.7209 (t70)
REVERT: R  126 TRP cc_start: 0.7101 (m100) cc_final: 0.6868 (m100)
REVERT: R  175 TRP cc_start: 0.4748 (t-100) cc_final: 0.4004 (t-100)
REVERT: R  255 ILE cc_start: 0.7614 (pt) cc_final: 0.7364 (mm)
REVERT: R  308 MET cc_start: 0.6626 (ppp) cc_final: 0.6347 (ppp)
REVERT: R  309 MET cc_start: 0.6719 (mpp) cc_final: 0.6179 (mpp)
REVERT: A   24 ARG cc_start: 0.6971 (mmp-170) cc_final: 0.6704 (mmp-170)
REVERT: A  139 CYS cc_start: 0.7545 (m) cc_final: 0.7336 (m)
REVERT: A  178 ARG cc_start: 0.6639 (tpt170) cc_final: 0.6406 (ttm110)
REVERT: A  341 ASP cc_start: 0.6784 (p0) cc_final: 0.6328 (t70)
REVERT: B   75 GLN cc_start: 0.7038 (mt0) cc_final: 0.6418 (tm-30)
REVERT: B  254 ASP cc_start: 0.7176 (t0) cc_final: 0.6773 (t0)
REVERT: B  331 SER cc_start: 0.8968 (t) cc_final: 0.8543 (m)
REVERT: G   28 ILE cc_start: 0.8445 (mm) cc_final: 0.8207 (tt)
REVERT: G   38 MET cc_start: 0.6691 (ppp) cc_final: 0.6481 (tpt)
REVERT: L  141 TYR cc_start: 0.5183 (m-10) cc_final: 0.4673 (m-80)
REVERT: H  112 TYR cc_start: 0.5971 (m-10) cc_final: 0.5014 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 217
  average time/residue: 0.0977
  time to fit residues: 31.2752
Evaluate side-chains
  163 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 162
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 43 optimal weight:    0.2980
   chunk 99 optimal weight:    0.7980
   chunk 18 optimal weight:    6.9990
   chunk 142 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9980
   chunk 104 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0030
   chunk 53 optimal weight:    0.4980
   chunk 46 optimal weight:   10.0000
   overall best weight:    0.5190

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

Flipped N/Q/H residues before XYZ refinement:
R  78 ASN
** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
** G  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  91 GLN
L 159 ASN
L 199 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.128310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.107113 restraints weight = 31710.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.106092 restraints weight = 35581.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.107185 restraints weight = 29126.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.107394 restraints weight = 21065.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.107704 restraints weight = 20210.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6730
moved from start:          0.3711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  12107  Z= 0.116
  Angle     :  0.618  11.619  16430  Z= 0.320
  Chirality :  0.043   0.197   1844
  Planarity :  0.004   0.085   2089
  Dihedral  :  5.248  52.890   1685
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.20), residues: 1504
  helix:  0.28 (0.22), residues: 511
  sheet:  0.14 (0.31), residues: 261
  loop : -1.20 (0.21), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 109 
 TYR   0.026   0.001   TYR R 257 
 PHE   0.021   0.002   PHE R  91 
 TRP   0.019   0.001   TRP R  35 
 HIS   0.009   0.001   HIS L 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (12099)
  covalent geometry    : angle       0.61576 (16412)
  SS BOND              : bond        0.00278 (    6)
  SS BOND              : angle       1.29949 (   12)
  hydrogen bonds       : bond        0.04469 (  515)
  hydrogen bonds       : angle       5.01735 ( 1488)
  link_BETA1-4         : bond        0.00044 (    1)
  link_BETA1-4         : angle       1.55546 (    3)
  link_NAG-ASN         : bond        0.00388 (    1)
  link_NAG-ASN         : angle       2.53457 (    3)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   37 PHE cc_start: 0.8088 (p90) cc_final: 0.7806 (p90)
REVERT: R  175 TRP cc_start: 0.4697 (t-100) cc_final: 0.3944 (t-100)
REVERT: R  253 MET cc_start: 0.7811 (tpp) cc_final: 0.7454 (tpp)
REVERT: R  255 ILE cc_start: 0.7552 (pt) cc_final: 0.7329 (mm)
REVERT: R  308 MET cc_start: 0.6532 (ppp) cc_final: 0.6127 (ppp)
REVERT: A   88 MET cc_start: 0.7854 (ppp) cc_final: 0.7310 (ppp)
REVERT: A  309 ASP cc_start: 0.7292 (p0) cc_final: 0.6995 (p0)
REVERT: B  188 MET cc_start: 0.8676 (mmm) cc_final: 0.8353 (mmm)
REVERT: B  254 ASP cc_start: 0.7186 (t0) cc_final: 0.6646 (t0)
REVERT: B  260 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8288 (tm-30)
REVERT: B  331 SER cc_start: 0.8779 (t) cc_final: 0.8557 (m)
REVERT: G   28 ILE cc_start: 0.8384 (mm) cc_final: 0.8094 (tt)
REVERT: G   38 MET cc_start: 0.6682 (ppp) cc_final: 0.6442 (tpt)
REVERT: L  141 TYR cc_start: 0.5193 (m-10) cc_final: 0.4684 (m-80)
REVERT: H  112 TYR cc_start: 0.5858 (m-10) cc_final: 0.5088 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.0950
  time to fit residues: 31.1900
Evaluate side-chains
  162 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 129 optimal weight:    8.9990
   chunk 30 optimal weight:    0.5980
   chunk 82 optimal weight:    0.2980
   chunk 67 optimal weight:    0.6980
   chunk 131 optimal weight:    8.9990
   chunk 31 optimal weight:    1.9990
   chunk 139 optimal weight:    9.9990
   chunk 143 optimal weight:    7.9990
   chunk 84 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
R  78 ASN
R 237 GLN
** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 HIS
B 340 ASN
** G  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 159 ASN
L 199 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.127600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.106528 restraints weight = 32062.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.105519 restraints weight = 33121.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.106481 restraints weight = 30387.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.106724 restraints weight = 22513.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.107033 restraints weight = 21079.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6753
moved from start:          0.3958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12107  Z= 0.124
  Angle     :  0.626  11.810  16430  Z= 0.325
  Chirality :  0.043   0.184   1844
  Planarity :  0.004   0.082   2089
  Dihedral  :  5.053  41.265   1685
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.64 %
    Favored  : 97.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.20), residues: 1504
  helix:  0.22 (0.22), residues: 514
  sheet:  0.08 (0.31), residues: 270
  loop : -1.17 (0.21), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 176 
 TYR   0.030   0.001   TYR A  69 
 PHE   0.038   0.002   PHE A 108 
 TRP   0.016   0.001   TRP R  35 
 HIS   0.009   0.001   HIS L 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (12099)
  covalent geometry    : angle       0.62508 (16412)
  SS BOND              : bond        0.00330 (    6)
  SS BOND              : angle       0.99421 (   12)
  hydrogen bonds       : bond        0.04394 (  515)
  hydrogen bonds       : angle       4.99923 ( 1488)
  link_BETA1-4         : bond        0.00387 (    1)
  link_BETA1-4         : angle       1.60014 (    3)
  link_NAG-ASN         : bond        0.00214 (    1)
  link_NAG-ASN         : angle       2.02083 (    3)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 216
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   37 PHE cc_start: 0.8139 (p90) cc_final: 0.7829 (p90)
REVERT: R  175 TRP cc_start: 0.4567 (t-100) cc_final: 0.3696 (t60)
REVERT: R  308 MET cc_start: 0.6198 (ppp) cc_final: 0.5810 (ppp)
REVERT: R  312 GLN cc_start: 0.8305 (mt0) cc_final: 0.7799 (mt0)
REVERT: A   82 ILE cc_start: 0.8925 (mt) cc_final: 0.8710 (pt)
REVERT: A   88 MET cc_start: 0.7970 (ppp) cc_final: 0.7442 (ppp)
REVERT: A  272 ASP cc_start: 0.6625 (p0) cc_final: 0.6424 (p0)
REVERT: A  295 THR cc_start: 0.7156 (m) cc_final: 0.6490 (p)
REVERT: A  298 GLU cc_start: 0.7966 (pm20) cc_final: 0.7734 (pm20)
REVERT: B  254 ASP cc_start: 0.7404 (t0) cc_final: 0.6759 (t0)
REVERT: B  331 SER cc_start: 0.8806 (t) cc_final: 0.8512 (m)
REVERT: G   28 ILE cc_start: 0.8426 (mm) cc_final: 0.8176 (tt)
REVERT: G   38 MET cc_start: 0.6740 (ppp) cc_final: 0.6494 (tpt)
REVERT: L  141 TYR cc_start: 0.5229 (m-10) cc_final: 0.4478 (m-80)
REVERT: H  105 TYR cc_start: 0.5923 (p90) cc_final: 0.5668 (p90)
REVERT: H  112 TYR cc_start: 0.5843 (m-10) cc_final: 0.5074 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 218
  average time/residue: 0.0966
  time to fit residues: 31.3223
Evaluate side-chains
  167 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 125 optimal weight:    0.2980
   chunk 34 optimal weight:    0.7980
   chunk 119 optimal weight:    9.9990
   chunk 149 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 129 optimal weight:    8.9990
   chunk 79 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9980
   chunk 136 optimal weight:    2.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
R  78 ASN
** R 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 237 GLN
** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 164 GLN
B 156 GLN
B 225 HIS
B 340 ASN
** G  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 159 ASN
L 199 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.127774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.107726 restraints weight = 31862.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.106379 restraints weight = 40779.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.107668 restraints weight = 33201.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.107843 restraints weight = 22489.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.108208 restraints weight = 21654.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6714
moved from start:          0.4095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12107  Z= 0.120
  Angle     :  0.624  11.976  16430  Z= 0.321
  Chirality :  0.043   0.180   1844
  Planarity :  0.004   0.081   2089
  Dihedral  :  4.825  27.808   1685
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.56 %
    Favored  : 97.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.21), residues: 1504
  helix:  0.34 (0.22), residues: 513
  sheet:  0.08 (0.31), residues: 278
  loop : -1.20 (0.21), residues: 713

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  62 
 TYR   0.029   0.001   TYR A  69 
 PHE   0.032   0.002   PHE A 108 
 TRP   0.014   0.001   TRP R  35 
 HIS   0.010   0.001   HIS L 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (12099)
  covalent geometry    : angle       0.62324 (16412)
  SS BOND              : bond        0.00324 (    6)
  SS BOND              : angle       0.73031 (   12)
  hydrogen bonds       : bond        0.04320 (  515)
  hydrogen bonds       : angle       4.94601 ( 1488)
  link_BETA1-4         : bond        0.00048 (    1)
  link_BETA1-4         : angle       1.64526 (    3)
  link_NAG-ASN         : bond        0.00363 (    1)
  link_NAG-ASN         : angle       1.76804 (    3)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 212
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  175 TRP cc_start: 0.4631 (t-100) cc_final: 0.3735 (t60)
REVERT: R  207 MET cc_start: 0.7001 (mtm) cc_final: 0.6760 (ptt)
REVERT: R  308 MET cc_start: 0.6119 (ppp) cc_final: 0.5809 (ppp)
REVERT: R  312 GLN cc_start: 0.8268 (mt0) cc_final: 0.7812 (mt0)
REVERT: A   88 MET cc_start: 0.7808 (ppp) cc_final: 0.7431 (ppp)
REVERT: B   76 ASP cc_start: 0.7471 (p0) cc_final: 0.6910 (p0)
REVERT: B  254 ASP cc_start: 0.7176 (t0) cc_final: 0.6660 (t0)
REVERT: B  331 SER cc_start: 0.8882 (t) cc_final: 0.8398 (m)
REVERT: G   28 ILE cc_start: 0.8490 (mm) cc_final: 0.8249 (tt)
REVERT: L  141 TYR cc_start: 0.4960 (m-10) cc_final: 0.4229 (m-80)
REVERT: L  166 GLU cc_start: 0.5355 (mt-10) cc_final: 0.5139 (mt-10)
REVERT: H  112 TYR cc_start: 0.5670 (m-10) cc_final: 0.4918 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 214
  average time/residue: 0.0965
  time to fit residues: 30.7717
Evaluate side-chains
  158 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 1 optimal weight:    0.4980
   chunk 20 optimal weight:    0.8980
   chunk 136 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 131 optimal weight:    3.9990
   chunk 16 optimal weight:   10.0000
   chunk 139 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 118 optimal weight:    3.9990
   chunk 146 optimal weight:    3.9990
   overall best weight:    2.6786

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

Flipped N/Q/H residues before XYZ refinement:
R 200 ASN
B 340 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 159 ASN
L 167 GLN
L 199 HIS
L 200 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.122556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.103237 restraints weight = 32198.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.102007 restraints weight = 42440.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.102947 restraints weight = 36070.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.103285 restraints weight = 25063.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.103590 restraints weight = 23712.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6837
moved from start:          0.4504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  12107  Z= 0.212
  Angle     :  0.751  14.240  16430  Z= 0.397
  Chirality :  0.047   0.201   1844
  Planarity :  0.005   0.071   2089
  Dihedral  :  5.420  32.138   1685
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.20), residues: 1504
  helix: -0.20 (0.21), residues: 526
  sheet: -0.21 (0.32), residues: 268
  loop : -1.43 (0.21), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B   8 
 TYR   0.032   0.002   TYR L 141 
 PHE   0.031   0.003   PHE R 115 
 TRP   0.019   0.002   TRP R  35 
 HIS   0.012   0.002   HIS L 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 (12099)
  covalent geometry    : angle       0.74941 (16412)
  SS BOND              : bond        0.00575 (    6)
  SS BOND              : angle       1.47923 (   12)
  hydrogen bonds       : bond        0.05218 (  515)
  hydrogen bonds       : angle       5.32670 ( 1488)
  link_BETA1-4         : bond        0.00657 (    1)
  link_BETA1-4         : angle       1.86256 (    3)
  link_NAG-ASN         : bond        0.00330 (    1)
  link_NAG-ASN         : angle       0.61105 (    3)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   86 MET cc_start: 0.7544 (tmm) cc_final: 0.6942 (ttt)
REVERT: R  207 MET cc_start: 0.6910 (mtm) cc_final: 0.6530 (ptt)
REVERT: R  308 MET cc_start: 0.6098 (ppp) cc_final: 0.5792 (ppp)
REVERT: B  254 ASP cc_start: 0.7349 (t0) cc_final: 0.6863 (t0)
REVERT: B  331 SER cc_start: 0.9051 (t) cc_final: 0.8609 (m)
REVERT: G   28 ILE cc_start: 0.8460 (mm) cc_final: 0.8256 (tt)
REVERT: L  141 TYR cc_start: 0.4773 (m-10) cc_final: 0.4539 (m-80)
REVERT: H  112 TYR cc_start: 0.6159 (m-10) cc_final: 0.5649 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.0948
  time to fit residues: 27.9945
Evaluate side-chains
  148 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 129 optimal weight:    6.9990
   chunk 145 optimal weight:    6.9990
   chunk 148 optimal weight:   10.0000
   chunk 104 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 118 optimal weight:    0.5980
   chunk 88 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 81 optimal weight:    3.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
R 237 GLN
B 225 HIS
B 340 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 159 ASN
L 167 GLN
L 199 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.124220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.104667 restraints weight = 32052.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.103733 restraints weight = 41418.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.104777 restraints weight = 33146.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.104928 restraints weight = 23846.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.105110 restraints weight = 23796.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6805
moved from start:          0.4537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12107  Z= 0.158
  Angle     :  0.697  13.204  16430  Z= 0.364
  Chirality :  0.045   0.163   1844
  Planarity :  0.005   0.073   2089
  Dihedral  :  5.254  30.867   1685
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.78 %
    Favored  : 99.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.20), residues: 1504
  helix:  0.05 (0.22), residues: 519
  sheet: -0.24 (0.32), residues: 270
  loop : -1.35 (0.21), residues: 715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG R 177 
 TYR   0.025   0.002   TYR R 257 
 PHE   0.032   0.002   PHE A 108 
 TRP   0.019   0.002   TRP R  35 
 HIS   0.012   0.001   HIS L 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (12099)
  covalent geometry    : angle       0.69664 (16412)
  SS BOND              : bond        0.00406 (    6)
  SS BOND              : angle       1.06820 (   12)
  hydrogen bonds       : bond        0.04853 (  515)
  hydrogen bonds       : angle       5.12257 ( 1488)
  link_BETA1-4         : bond        0.00156 (    1)
  link_BETA1-4         : angle       1.68700 (    3)
  link_NAG-ASN         : bond        0.00427 (    1)
  link_NAG-ASN         : angle       1.00737 (    3)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 188
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  207 MET cc_start: 0.6711 (mtm) cc_final: 0.6494 (ptt)
REVERT: A   88 MET cc_start: 0.7828 (ppp) cc_final: 0.7352 (ppp)
REVERT: B  254 ASP cc_start: 0.7087 (t0) cc_final: 0.6658 (t0)
REVERT: B  331 SER cc_start: 0.9059 (t) cc_final: 0.8592 (m)
REVERT: G   28 ILE cc_start: 0.8413 (mm) cc_final: 0.8092 (tt)
REVERT: H  112 TYR cc_start: 0.5977 (m-10) cc_final: 0.5543 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 189
  average time/residue: 0.0920
  time to fit residues: 26.4321
Evaluate side-chains
  141 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 99 optimal weight:    0.0670
   chunk 115 optimal weight:    0.9990
   chunk 117 optimal weight:    0.9980
   chunk 95 optimal weight:    5.9990
   chunk 122 optimal weight:   10.0000
   chunk 109 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 98 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 110 optimal weight:    0.9990
   chunk 148 optimal weight:    0.7980
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
R 237 GLN
R 302 ASN
A 306 GLN
B 225 HIS
B 340 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 159 ASN
L 199 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.126651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.107468 restraints weight = 31960.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.106562 restraints weight = 40694.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.107442 restraints weight = 35242.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.107580 restraints weight = 25063.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.107864 restraints weight = 23586.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6728
moved from start:          0.4620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  12107  Z= 0.119
  Angle     :  0.646  13.322  16430  Z= 0.333
  Chirality :  0.043   0.170   1844
  Planarity :  0.004   0.069   2089
  Dihedral  :  4.891  26.296   1685
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.47 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.21), residues: 1504
  helix:  0.27 (0.22), residues: 512
  sheet: -0.08 (0.32), residues: 272
  loop : -1.31 (0.21), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 177 
 TYR   0.027   0.001   TYR R 257 
 PHE   0.036   0.002   PHE R  37 
 TRP   0.014   0.001   TRP R  35 
 HIS   0.013   0.001   HIS L 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (12099)
  covalent geometry    : angle       0.64536 (16412)
  SS BOND              : bond        0.00303 (    6)
  SS BOND              : angle       0.79310 (   12)
  hydrogen bonds       : bond        0.04405 (  515)
  hydrogen bonds       : angle       4.92962 ( 1488)
  link_BETA1-4         : bond        0.00091 (    1)
  link_BETA1-4         : angle       1.73037 (    3)
  link_NAG-ASN         : bond        0.00429 (    1)
  link_NAG-ASN         : angle       1.55828 (    3)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 198
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   83 ASP cc_start: 0.6528 (t0) cc_final: 0.5719 (t0)
REVERT: R  207 MET cc_start: 0.7029 (mtm) cc_final: 0.6686 (ptt)
REVERT: R  312 GLN cc_start: 0.8268 (mt0) cc_final: 0.7879 (mt0)
REVERT: A   88 MET cc_start: 0.7882 (ppp) cc_final: 0.7423 (ppp)
REVERT: A  309 ASP cc_start: 0.7089 (p0) cc_final: 0.6798 (p0)
REVERT: B   76 ASP cc_start: 0.7602 (p0) cc_final: 0.7151 (p0)
REVERT: B  186 ASP cc_start: 0.8174 (t0) cc_final: 0.7941 (t0)
REVERT: B  254 ASP cc_start: 0.6802 (t0) cc_final: 0.6566 (t0)
REVERT: B  260 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7902 (tm-30)
REVERT: B  264 TYR cc_start: 0.7397 (m-10) cc_final: 0.6901 (m-10)
REVERT: B  331 SER cc_start: 0.8922 (t) cc_final: 0.8381 (m)
REVERT: G   28 ILE cc_start: 0.8434 (mm) cc_final: 0.8040 (tt)
REVERT: L    5 MET cc_start: 0.4993 (ppp) cc_final: 0.4670 (ppp)
REVERT: H  112 TYR cc_start: 0.5809 (m-10) cc_final: 0.5277 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 199
  average time/residue: 0.0911
  time to fit residues: 27.3380
Evaluate side-chains
  151 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 44 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 143 optimal weight:    0.3980
   chunk 81 optimal weight:    0.3980
   chunk 134 optimal weight:    9.9990
   chunk 14 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 59 optimal weight:    0.2980
   chunk 135 optimal weight:    6.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
R  78 ASN
R 237 GLN
B 225 HIS
B 340 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 159 ASN
L 199 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.125935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.105960 restraints weight = 32058.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.104541 restraints weight = 38294.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.105339 restraints weight = 36421.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.105689 restraints weight = 25735.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.105922 restraints weight = 24492.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6781
moved from start:          0.4715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12107  Z= 0.128
  Angle     :  0.651  12.550  16430  Z= 0.337
  Chirality :  0.044   0.182   1844
  Planarity :  0.004   0.068   2089
  Dihedral  :  4.817  24.513   1685
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.39 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.81 (0.21), residues: 1504
  helix:  0.27 (0.22), residues: 519
  sheet: -0.12 (0.32), residues: 278
  loop : -1.28 (0.22), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  62 
 TYR   0.034   0.001   TYR R 257 
 PHE   0.037   0.002   PHE R  37 
 TRP   0.013   0.001   TRP R  35 
 HIS   0.012   0.001   HIS L 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (12099)
  covalent geometry    : angle       0.65060 (16412)
  SS BOND              : bond        0.00325 (    6)
  SS BOND              : angle       0.84538 (   12)
  hydrogen bonds       : bond        0.04403 (  515)
  hydrogen bonds       : angle       4.88296 ( 1488)
  link_BETA1-4         : bond        0.00171 (    1)
  link_BETA1-4         : angle       1.68239 (    3)
  link_NAG-ASN         : bond        0.00355 (    1)
  link_NAG-ASN         : angle       1.25822 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1736.03 seconds
wall clock time: 30 minutes 58.67 seconds (1858.67 seconds total)