Starting phenix.real_space_refine
on Fri Sep 11 21:56:55 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6cmo_7517/09_2026/6cmo_7517.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6cmo_7517/09_2026/6cmo_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_7517/09_2026/6cmo_7517.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6cmo_7517/09_2026/6cmo_7517.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6cmo_7517/09_2026/6cmo_7517.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6cmo_7517/09_2026/6cmo_7517.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/6cmo_7517/09_2026/6cmo_7517.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6cmo_7517/09_2026/6cmo_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-2.2.1-6174/lib/python3.11/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 chiralities: 2
  Time building chain proxies: 3.07, per 1000 atoms: 0.26
  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: 1.00
  Conformation dependent library (CDL) restraints added in 658.4 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: 0.36
  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: 1.96

  Time building geometry restraints manager: 1.30 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: 6735
       14.99 -    29.97: 342
       29.97 -    44.96: 90
       44.96 -    59.95: 11
       59.95 -    74.93: 7
  Dihedral angle restraints: 7185
    sinusoidal: 2768
      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 7182 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:             1.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.520
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.670
-------------------------------------------------------------------------------
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  : 10.434  74.935   4327
  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/Z
  covalent geometry    : bond        0.00422 /  0.22 (12099)
  covalent geometry    : angle       0.99534 /  0.53 (16412)
  SS BOND              : bond        0.00235 /  0.12 (    6)
  SS BOND              : angle       2.13738 /  1.11 (   12)
  hydrogen bonds       : bond        0.18521 / 11.92 (  515)
  hydrogen bonds       : angle       9.45612 /  6.87 ( 1488)
  link_BETA1-4         : bond        0.00611 /  0.32 (    1)
  link_BETA1-4         : angle       1.95576 /  1.03 (    3)
  link_NAG-ASN         : bond        0.03150 /  1.66 (    1)
  link_NAG-ASN         : angle      12.68548 /  7.25 (    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  : 0.466 
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: 0.4901 (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: 0.5915 (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: 0.4329 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 330
  average time/residue: 0.1293
  time to fit residues: 58.5402
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  : 0.450 
-------------------------------------------------------------------------------
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...
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 138 ASN
L 159 ASN
L 199 HIS
L 211 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.124953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.101662 restraints weight = 32358.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.100708 restraints weight = 27312.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.101481 restraints weight = 26201.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.101741 restraints weight = 19497.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.101862 restraints weight = 19657.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6864
moved from start:          0.2870

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= 0.215
  Angle     :  0.746  10.110  16430  Z= 0.397
  Chirality :  0.047   0.178   1844
  Planarity :  0.006   0.089   2089
  Dihedral  :  5.880  51.170   1643
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  4.81 %
    Favored  : 94.65 %
  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: -1.27 (0.19), residues: 1504
  helix: -0.42 (0.21), residues: 528
  sheet: -0.11 (0.29), residues: 263
  loop : -1.40 (0.19), residues: 713

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG R 177 
 TYR   0.036   0.003   TYR A 290 
 PHE   0.027   0.003   PHE B 241 
 TRP   0.021   0.002   TRP R  35 
 HIS   0.008   0.002   HIS H  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00470 /  0.21 (12099)
  covalent geometry    : angle       0.74395 /  0.40 (16412)
  SS BOND              : bond        0.00537 /  0.29 (    6)
  SS BOND              : angle       1.29437 /  0.62 (   12)
  hydrogen bonds       : bond        0.05629 /  3.67 (  515)
  hydrogen bonds       : angle       6.06640 /  4.41 ( 1488)
  link_BETA1-4         : bond        0.00949 /  0.50 (    1)
  link_BETA1-4         : angle       1.36092 /  0.70 (    3)
  link_NAG-ASN         : bond        0.00743 /  0.39 (    1)
  link_NAG-ASN         : angle       3.45799 /  1.86 (    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
  227 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 220
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  175 TRP cc_start: 0.4627 (t-100) cc_final: 0.3810 (t-100)
REVERT: A  139 CYS cc_start: 0.7570 (m) cc_final: 0.7341 (m)
REVERT: A  302 TYR cc_start: 0.4412 (t80) cc_final: 0.3431 (t80)
REVERT: A  346 ASN cc_start: 0.7024 (t0) cc_final: 0.6764 (t0)
REVERT: A  353 LEU cc_start: 0.7807 (mp) cc_final: 0.7559 (mp)
REVERT: B   75 GLN cc_start: 0.7031 (mt0) cc_final: 0.6443 (tm-30)
REVERT: B  254 ASP cc_start: 0.7254 (t0) cc_final: 0.6963 (t0)
REVERT: B  331 SER cc_start: 0.8995 (t) cc_final: 0.8534 (m)
REVERT: G   28 ILE cc_start: 0.8417 (mm) cc_final: 0.8059 (tt)
REVERT: G   38 MET cc_start: 0.6733 (ppp) cc_final: 0.6341 (tpt)
  outliers start: 7
  outliers final: 3
  residues processed: 225
  average time/residue: 0.1097
  time to fit residues: 35.9581
Evaluate side-chains
  155 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 152
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 19 optimal weight:    7.9990
   chunk 4 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 37 optimal weight:    8.9990
   chunk 56 optimal weight:    0.9990
   chunk 129 optimal weight:    1.9990
   chunk 104 optimal weight:    5.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 138 ASN
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 = 0.3907 r_free = 0.3907 target = 0.127897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.106775 restraints weight = 31633.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.105541 restraints weight = 36741.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.106860 restraints weight = 29159.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.107319 restraints weight = 20856.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.107543 restraints weight = 19766.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6715
moved from start:          0.3086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12107  Z= 0.126
  Angle     :  0.637   9.619  16430  Z= 0.333
  Chirality :  0.043   0.182   1844
  Planarity :  0.005   0.077   2089
  Dihedral  :  5.271  44.914   1643
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  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: -0.86 (0.20), residues: 1504
  helix:  0.08 (0.22), residues: 516
  sheet:  0.17 (0.30), residues: 268
  loop : -1.32 (0.20), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  62 
 TYR   0.022   0.002   TYR R 257 
 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/Z
  covalent geometry    : bond        0.00263 /  0.13 (12099)
  covalent geometry    : angle       0.63573 /  0.33 (16412)
  SS BOND              : bond        0.00434 /  0.21 (    6)
  SS BOND              : angle       0.86253 /  0.39 (   12)
  hydrogen bonds       : bond        0.04852 /  3.12 (  515)
  hydrogen bonds       : angle       5.47380 /  3.99 ( 1488)
  link_BETA1-4         : bond        0.00017 /  0.01 (    1)
  link_BETA1-4         : angle       1.17439 /  0.64 (    3)
  link_NAG-ASN         : bond        0.00211 /  0.11 (    1)
  link_NAG-ASN         : angle       3.18800 /  1.68 (    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
  216 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   83 ASP cc_start: 0.7447 (t0) cc_final: 0.7201 (t0)
REVERT: R  175 TRP cc_start: 0.4797 (t-100) cc_final: 0.4272 (t-100)
REVERT: R  255 ILE cc_start: 0.7570 (pt) cc_final: 0.7319 (mm)
REVERT: R  257 TYR cc_start: 0.7486 (m-10) cc_final: 0.5843 (m-80)
REVERT: A   24 ARG cc_start: 0.6927 (mmp-170) cc_final: 0.6602 (mmp-170)
REVERT: A   74 TYR cc_start: 0.7034 (m-80) cc_final: 0.6797 (m-80)
REVERT: A  178 ARG cc_start: 0.6476 (tpt170) cc_final: 0.6191 (ptp-110)
REVERT: A  295 THR cc_start: 0.6844 (m) cc_final: 0.6590 (m)
REVERT: A  296 TYR cc_start: 0.5777 (p90) cc_final: 0.5500 (p90)
REVERT: A  302 TYR cc_start: 0.4650 (t80) cc_final: 0.4276 (t80)
REVERT: B   75 GLN cc_start: 0.6621 (mt0) cc_final: 0.5966 (tm-30)
REVERT: B  186 ASP cc_start: 0.8222 (t0) cc_final: 0.7859 (t0)
REVERT: B  228 ASP cc_start: 0.7997 (m-30) cc_final: 0.7679 (m-30)
REVERT: B  254 ASP cc_start: 0.7047 (t0) cc_final: 0.6807 (t70)
REVERT: B  331 SER cc_start: 0.8928 (t) cc_final: 0.8499 (m)
REVERT: G   28 ILE cc_start: 0.8398 (mm) cc_final: 0.7940 (tt)
REVERT: G   38 MET cc_start: 0.6738 (ppp) cc_final: 0.6501 (tpt)
REVERT: L  141 TYR cc_start: 0.5152 (m-10) cc_final: 0.4877 (m-80)
REVERT: H  105 TYR cc_start: 0.5706 (p90) cc_final: 0.5487 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 216
  average time/residue: 0.1046
  time to fit residues: 33.1581
Evaluate side-chains
  160 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 106 optimal weight:    6.9990
   chunk 64 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 75 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 124 optimal weight:   10.0000
   chunk 41 optimal weight:    0.8980
   overall best weight:    1.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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  91 GLN
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 = 0.3870 r_free = 0.3870 target = 0.125407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.103722 restraints weight = 32218.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.101834 restraints weight = 36621.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.103117 restraints weight = 30611.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.103476 restraints weight = 21593.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.103724 restraints weight = 20595.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6817
moved from start:          0.3551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12107  Z= 0.153
  Angle     :  0.645   9.260  16430  Z= 0.343
  Chirality :  0.044   0.178   1844
  Planarity :  0.005   0.072   2089
  Dihedral  :  5.162  41.224   1643
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.95 %
    Favored  : 95.97 %
  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: -0.90 (0.20), residues: 1504
  helix:  0.11 (0.22), residues: 511
  sheet: -0.10 (0.30), residues: 292
  loop : -1.31 (0.21), residues: 701

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L 109 
 TYR   0.032   0.002   TYR A  69 
 PHE   0.023   0.002   PHE R 221 
 TRP   0.037   0.002   TRP R  35 
 HIS   0.008   0.001   HIS L 199 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.15 (12099)
  covalent geometry    : angle       0.64391 /  0.34 (16412)
  SS BOND              : bond        0.00853 /  0.33 (    6)
  SS BOND              : angle       1.03772 /  0.50 (   12)
  hydrogen bonds       : bond        0.04843 /  3.14 (  515)
  hydrogen bonds       : angle       5.35833 /  3.93 ( 1488)
  link_BETA1-4         : bond        0.00286 /  0.15 (    1)
  link_BETA1-4         : angle       1.27996 /  0.67 (    3)
  link_NAG-ASN         : bond        0.00158 /  0.08 (    1)
  link_NAG-ASN         : angle       2.03884 /  1.09 (    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
  212 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 211
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   83 ASP cc_start: 0.7477 (t0) cc_final: 0.7209 (t70)
REVERT: R  175 TRP cc_start: 0.4761 (t-100) cc_final: 0.4030 (t-100)
REVERT: R  257 TYR cc_start: 0.7284 (m-10) cc_final: 0.7060 (m-80)
REVERT: R  308 MET cc_start: 0.6629 (ppp) cc_final: 0.6413 (ppp)
REVERT: A   24 ARG cc_start: 0.6966 (mmp-170) cc_final: 0.6648 (mmp-170)
REVERT: A  139 CYS cc_start: 0.7583 (m) cc_final: 0.7378 (m)
REVERT: A  302 TYR cc_start: 0.4761 (t80) cc_final: 0.4560 (t80)
REVERT: B  186 ASP cc_start: 0.8186 (t0) cc_final: 0.7908 (t0)
REVERT: B  188 MET cc_start: 0.8729 (mmm) cc_final: 0.8413 (mmm)
REVERT: B  254 ASP cc_start: 0.7295 (t0) cc_final: 0.6855 (t0)
REVERT: B  331 SER cc_start: 0.8974 (t) cc_final: 0.8610 (m)
REVERT: G   28 ILE cc_start: 0.8472 (mm) cc_final: 0.8031 (tt)
REVERT: G   38 MET cc_start: 0.6743 (ppp) cc_final: 0.6514 (tpt)
REVERT: L  141 TYR cc_start: 0.5337 (m-10) cc_final: 0.4865 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 212
  average time/residue: 0.0987
  time to fit residues: 31.4033
Evaluate side-chains
  160 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 159
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 99 optimal weight:    0.5980
   chunk 18 optimal weight:    4.9990
   chunk 142 optimal weight:    0.7980
   chunk 98 optimal weight:    5.9990
   chunk 104 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0980
   chunk 53 optimal weight:    0.1980
   chunk 46 optimal weight:    6.9990
   overall best weight:    0.4180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 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 = 0.3903 r_free = 0.3903 target = 0.127857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.106480 restraints weight = 31599.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.104789 restraints weight = 41103.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.105843 restraints weight = 31825.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.107133 restraints weight = 24291.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.107245 restraints weight = 20385.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6719
moved from start:          0.3620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12107  Z= 0.119
  Angle     :  0.622  12.817  16430  Z= 0.321
  Chirality :  0.043   0.171   1844
  Planarity :  0.004   0.071   2089
  Dihedral  :  4.871  36.204   1643
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  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:  0.31 (0.22), residues: 510
  sheet:  0.05 (0.31), residues: 271
  loop : -1.21 (0.21), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 177 
 TYR   0.016   0.001   TYR A 296 
 PHE   0.022   0.002   PHE R  91 
 TRP   0.017   0.001   TRP R  35 
 HIS   0.009   0.001   HIS L 199 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.12 (12099)
  covalent geometry    : angle       0.62060 /  0.32 (16412)
  SS BOND              : bond        0.01041 /  0.50 (    6)
  SS BOND              : angle       1.12131 /  0.49 (   12)
  hydrogen bonds       : bond        0.04533 /  2.92 (  515)
  hydrogen bonds       : angle       5.11193 /  3.75 ( 1488)
  link_BETA1-4         : bond        0.00482 /  0.25 (    1)
  link_BETA1-4         : angle       1.19527 /  0.63 (    3)
  link_NAG-ASN         : bond        0.00264 /  0.14 (    1)
  link_NAG-ASN         : angle       2.24901 /  1.20 (    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  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   37 PHE cc_start: 0.8008 (p90) cc_final: 0.7703 (p90)
REVERT: R  175 TRP cc_start: 0.4726 (t-100) cc_final: 0.3805 (t60)
REVERT: R  255 ILE cc_start: 0.7624 (pt) cc_final: 0.7347 (mm)
REVERT: R  308 MET cc_start: 0.6458 (ppp) cc_final: 0.6053 (ppp)
REVERT: A   24 ARG cc_start: 0.6922 (mmp-170) cc_final: 0.6711 (mmp-170)
REVERT: A   81 ILE cc_start: 0.8739 (tp) cc_final: 0.8494 (tp)
REVERT: A   88 MET cc_start: 0.7808 (ppp) cc_final: 0.7295 (ppp)
REVERT: A  295 THR cc_start: 0.6878 (m) cc_final: 0.6570 (m)
REVERT: B  186 ASP cc_start: 0.8109 (t0) cc_final: 0.7818 (t0)
REVERT: B  188 MET cc_start: 0.8747 (mmm) cc_final: 0.8389 (mmm)
REVERT: B  254 ASP cc_start: 0.7115 (t0) cc_final: 0.6816 (t0)
REVERT: B  331 SER cc_start: 0.8869 (t) cc_final: 0.8615 (m)
REVERT: L  141 TYR cc_start: 0.5309 (m-10) cc_final: 0.4740 (m-80)
REVERT: H  112 TYR cc_start: 0.6042 (m-10) cc_final: 0.5328 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.0996
  time to fit residues: 32.7515
Evaluate side-chains
  155 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 82 optimal weight:    0.0670
   chunk 67 optimal weight:    3.9990
   chunk 131 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9980
   chunk 139 optimal weight:    1.9990
   chunk 143 optimal weight:   30.0000
   chunk 84 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    1.3922

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  78 ASN
R 237 GLN
** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
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
L 200 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.126072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.104472 restraints weight = 31995.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.102117 restraints weight = 38329.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.103147 restraints weight = 31244.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.104731 restraints weight = 23374.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.104779 restraints weight = 19147.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6797
moved from start:          0.3975

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= 0.142
  Angle     :  0.652  11.152  16430  Z= 0.341
  Chirality :  0.044   0.167   1844
  Planarity :  0.005   0.070   2089
  Dihedral  :  4.931  33.503   1643
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.64 %
    Favored  : 96.28 %
  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: -0.91 (0.20), residues: 1504
  helix:  0.07 (0.22), residues: 518
  sheet: -0.17 (0.31), residues: 277
  loop : -1.25 (0.21), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  70 
 TYR   0.029   0.002   TYR A 302 
 PHE   0.026   0.002   PHE R  91 
 TRP   0.016   0.001   TRP R  35 
 HIS   0.010   0.001   HIS L 199 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.14 (12099)
  covalent geometry    : angle       0.65128 /  0.34 (16412)
  SS BOND              : bond        0.00416 /  0.21 (    6)
  SS BOND              : angle       1.16074 /  0.53 (   12)
  hydrogen bonds       : bond        0.04672 /  3.02 (  515)
  hydrogen bonds       : angle       5.10171 /  3.74 ( 1488)
  link_BETA1-4         : bond        0.00007 /  0.00 (    1)
  link_BETA1-4         : angle       1.37647 /  0.72 (    3)
  link_NAG-ASN         : bond        0.00197 /  0.10 (    1)
  link_NAG-ASN         : angle       1.57044 /  0.85 (    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
  210 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 209
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   37 PHE cc_start: 0.8165 (p90) cc_final: 0.7862 (p90)
REVERT: R  175 TRP cc_start: 0.4589 (t-100) cc_final: 0.3723 (t-100)
REVERT: R  308 MET cc_start: 0.6267 (ppp) cc_final: 0.5926 (ppp)
REVERT: A   24 ARG cc_start: 0.7067 (mmp-170) cc_final: 0.6849 (mmp-170)
REVERT: A   74 TYR cc_start: 0.7288 (m-80) cc_final: 0.7043 (m-80)
REVERT: A   88 MET cc_start: 0.7911 (ppp) cc_final: 0.7280 (ppp)
REVERT: B  186 ASP cc_start: 0.8151 (t0) cc_final: 0.7944 (t0)
REVERT: B  254 ASP cc_start: 0.7318 (t0) cc_final: 0.6816 (t0)
REVERT: B  331 SER cc_start: 0.8996 (t) cc_final: 0.8653 (m)
REVERT: L  141 TYR cc_start: 0.5235 (m-10) cc_final: 0.4483 (m-80)
REVERT: H  112 TYR cc_start: 0.5876 (m-10) cc_final: 0.4918 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 210
  average time/residue: 0.0934
  time to fit residues: 30.0883
Evaluate side-chains
  154 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 125 optimal weight:    0.0370
   chunk 34 optimal weight:    5.9990
   chunk 119 optimal weight:    8.9990
   chunk 149 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 129 optimal weight:    5.9990
   chunk 79 optimal weight:    3.9990
   chunk 55 optimal weight:    0.5980
   chunk 68 optimal weight:    1.9990
   chunk 136 optimal weight:    1.9990
   overall best weight:    1.1062

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  78 ASN
** R 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 237 GLN
** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 HIS
B 259 GLN
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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.126534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.105130 restraints weight = 32147.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.103820 restraints weight = 39730.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.105033 restraints weight = 32797.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.105251 restraints weight = 24927.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.105449 restraints weight = 23796.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6761
moved from start:          0.4118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12107  Z= 0.130
  Angle     :  0.648  12.273  16430  Z= 0.335
  Chirality :  0.043   0.166   1844
  Planarity :  0.005   0.084   2089
  Dihedral  :  4.876  30.822   1643
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.64 %
    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: -0.87 (0.20), residues: 1504
  helix:  0.17 (0.22), residues: 513
  sheet: -0.12 (0.31), residues: 279
  loop : -1.28 (0.21), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 176 
 TYR   0.023   0.001   TYR A 302 
 PHE   0.025   0.002   PHE R  91 
 TRP   0.015   0.001   TRP R  35 
 HIS   0.010   0.001   HIS L 199 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.13 (12099)
  covalent geometry    : angle       0.64756 /  0.33 (16412)
  SS BOND              : bond        0.00383 /  0.19 (    6)
  SS BOND              : angle       1.05068 /  0.49 (   12)
  hydrogen bonds       : bond        0.04520 /  2.93 (  515)
  hydrogen bonds       : angle       5.07394 /  3.75 ( 1488)
  link_BETA1-4         : bond        0.00041 /  0.02 (    1)
  link_BETA1-4         : angle       1.36931 /  0.73 (    3)
  link_NAG-ASN         : bond        0.00228 /  0.12 (    1)
  link_NAG-ASN         : angle       1.49216 /  0.80 (    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
  207 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 206
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  175 TRP cc_start: 0.4673 (t-100) cc_final: 0.3733 (t60)
REVERT: R  308 MET cc_start: 0.6161 (ppp) cc_final: 0.5872 (ppp)
REVERT: A   24 ARG cc_start: 0.7188 (mmp-170) cc_final: 0.6857 (mmp-170)
REVERT: A   88 MET cc_start: 0.7953 (ppp) cc_final: 0.7402 (ppp)
REVERT: B   76 ASP cc_start: 0.7488 (p0) cc_final: 0.6994 (p0)
REVERT: B  254 ASP cc_start: 0.7163 (t0) cc_final: 0.6723 (t0)
REVERT: B  331 SER cc_start: 0.8983 (t) cc_final: 0.8577 (m)
REVERT: L  141 TYR cc_start: 0.5248 (m-10) cc_final: 0.4550 (m-80)
REVERT: H  112 TYR cc_start: 0.5889 (m-10) cc_final: 0.4841 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 207
  average time/residue: 0.0972
  time to fit residues: 30.2656
Evaluate side-chains
  154 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 20 optimal weight:    0.9990
   chunk 136 optimal weight:    0.7980
   chunk 64 optimal weight:    0.6980
   chunk 131 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 139 optimal weight:    9.9990
   chunk 14 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   chunk 118 optimal weight:    0.7980
   chunk 146 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  78 ASN
** R 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 237 GLN
** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 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 = 0.3894 r_free = 0.3894 target = 0.127113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.106797 restraints weight = 31790.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.105029 restraints weight = 39535.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.106366 restraints weight = 32251.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.106635 restraints weight = 22436.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.106712 restraints weight = 23469.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6708
moved from start:          0.4240

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= 0.121
  Angle     :  0.646  12.551  16430  Z= 0.332
  Chirality :  0.044   0.160   1844
  Planarity :  0.004   0.083   2089
  Dihedral  :  4.741  27.529   1643
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.55 %
    Favored  : 98.37 %
  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: -0.82 (0.21), residues: 1504
  helix:  0.18 (0.22), residues: 519
  sheet: -0.06 (0.31), residues: 278
  loop : -1.25 (0.21), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  70 
 TYR   0.034   0.001   TYR L 141 
 PHE   0.026   0.002   PHE R  91 
 TRP   0.014   0.001   TRP R  35 
 HIS   0.011   0.001   HIS L 199 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.12 (12099)
  covalent geometry    : angle       0.64552 /  0.33 (16412)
  SS BOND              : bond        0.00336 /  0.17 (    6)
  SS BOND              : angle       1.03277 /  0.46 (   12)
  hydrogen bonds       : bond        0.04380 /  2.84 (  515)
  hydrogen bonds       : angle       4.98670 /  3.69 ( 1488)
  link_BETA1-4         : bond        0.00210 /  0.11 (    1)
  link_BETA1-4         : angle       1.36907 /  0.73 (    3)
  link_NAG-ASN         : bond        0.00312 /  0.16 (    1)
  link_NAG-ASN         : angle       1.52961 /  0.82 (    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
  209 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 208
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: R  175 TRP cc_start: 0.4681 (t-100) cc_final: 0.3784 (t60)
REVERT: R  207 MET cc_start: 0.7010 (mtm) cc_final: 0.6750 (ptt)
REVERT: R  308 MET cc_start: 0.6179 (ppp) cc_final: 0.5783 (ppp)
REVERT: R  312 GLN cc_start: 0.8289 (mt0) cc_final: 0.7813 (mt0)
REVERT: A   88 MET cc_start: 0.7867 (ppp) cc_final: 0.7376 (ppp)
REVERT: A  277 LYS cc_start: 0.8562 (mptt) cc_final: 0.8269 (mmmt)
REVERT: B   76 ASP cc_start: 0.7592 (p0) cc_final: 0.7144 (p0)
REVERT: B  186 ASP cc_start: 0.8073 (t0) cc_final: 0.7807 (t0)
REVERT: B  254 ASP cc_start: 0.7247 (t0) cc_final: 0.6695 (t0)
REVERT: B  331 SER cc_start: 0.8998 (t) cc_final: 0.8568 (m)
REVERT: H  112 TYR cc_start: 0.5727 (m-10) cc_final: 0.4749 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 209
  average time/residue: 0.0957
  time to fit residues: 30.0816
Evaluate side-chains
  157 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 145 optimal weight:    2.9990
   chunk 148 optimal weight:   10.0000
   chunk 104 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 71 optimal weight:    9.9990
   chunk 118 optimal weight:    0.9980
   chunk 88 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 81 optimal weight:    0.0570
   overall best weight:    1.6104

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  78 ASN
R 200 ASN
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 = 0.3868 r_free = 0.3868 target = 0.125357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.105040 restraints weight = 31959.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.103842 restraints weight = 42239.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.104970 restraints weight = 32862.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.105089 restraints weight = 25114.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.105268 restraints weight = 24445.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6763
moved from start:          0.4427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12107  Z= 0.155
  Angle     :  0.685  15.635  16430  Z= 0.356
  Chirality :  0.045   0.242   1844
  Planarity :  0.005   0.073   2089
  Dihedral  :  4.947  27.676   1643
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  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: -0.92 (0.21), residues: 1504
  helix:  0.08 (0.22), residues: 519
  sheet: -0.17 (0.32), residues: 274
  loop : -1.28 (0.21), residues: 711

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  70 
 TYR   0.017   0.002   TYR A  69 
 PHE   0.029   0.002   PHE R  91 
 TRP   0.018   0.002   TRP R  35 
 HIS   0.012   0.001   HIS L 199 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.15 (12099)
  covalent geometry    : angle       0.68470 /  0.36 (16412)
  SS BOND              : bond        0.00471 /  0.23 (    6)
  SS BOND              : angle       1.02765 /  0.47 (   12)
  hydrogen bonds       : bond        0.04774 /  3.05 (  515)
  hydrogen bonds       : angle       5.06552 /  3.74 ( 1488)
  link_BETA1-4         : bond        0.00108 /  0.06 (    1)
  link_BETA1-4         : angle       1.43566 /  0.75 (    3)
  link_NAG-ASN         : bond        0.00212 /  0.11 (    1)
  link_NAG-ASN         : angle       1.02408 /  0.56 (    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
  201 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   37 PHE cc_start: 0.8034 (p90) cc_final: 0.7826 (p90)
REVERT: R  163 MET cc_start: 0.4439 (ttm) cc_final: 0.4224 (ttm)
REVERT: R  175 TRP cc_start: 0.4771 (t-100) cc_final: 0.3764 (t60)
REVERT: R  207 MET cc_start: 0.6913 (mtm) cc_final: 0.6648 (ptt)
REVERT: R  308 MET cc_start: 0.5952 (ppp) cc_final: 0.5695 (ppp)
REVERT: A   88 MET cc_start: 0.7873 (ppp) cc_final: 0.7299 (ppp)
REVERT: B   76 ASP cc_start: 0.7681 (p0) cc_final: 0.7175 (p0)
REVERT: B  254 ASP cc_start: 0.7257 (t0) cc_final: 0.6769 (t0)
REVERT: B  331 SER cc_start: 0.8909 (t) cc_final: 0.8457 (m)
REVERT: H  112 TYR cc_start: 0.5797 (m-10) cc_final: 0.5059 (m-80)
REVERT: H  193 LEU cc_start: 0.5629 (pp) cc_final: 0.4233 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 201
  average time/residue: 0.0943
  time to fit residues: 28.5595
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  : 0.442 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 115 optimal weight:    0.1980
   chunk 117 optimal weight:    4.9990
   chunk 95 optimal weight:    0.7980
   chunk 122 optimal weight:    0.0170
   chunk 109 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 98 optimal weight:    6.9990
   chunk 27 optimal weight:    7.9990
   chunk 110 optimal weight:    3.9990
   chunk 148 optimal weight:    9.9990
   overall best weight:    0.7620

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  78 ASN
R 237 GLN
** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3892 r_free = 0.3892 target = 0.127055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.107522 restraints weight = 31820.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.106655 restraints weight = 40746.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.107492 restraints weight = 34259.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.107666 restraints weight = 24441.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.107928 restraints weight = 23430.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6682
moved from start:          0.4464

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= 0.121
  Angle     :  0.655  11.776  16430  Z= 0.337
  Chirality :  0.044   0.182   1844
  Planarity :  0.004   0.081   2089
  Dihedral  :  4.705  24.161   1643
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.62 %
    Favored  : 99.30 %
  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:  0.23 (0.22), residues: 518
  sheet: -0.10 (0.32), residues: 279
  loop : -1.27 (0.21), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  70 
 TYR   0.026   0.001   TYR A  69 
 PHE   0.027   0.002   PHE R  91 
 TRP   0.014   0.001   TRP R  35 
 HIS   0.013   0.001   HIS L 199 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.12 (12099)
  covalent geometry    : angle       0.65458 /  0.34 (16412)
  SS BOND              : bond        0.00284 /  0.14 (    6)
  SS BOND              : angle       0.85158 /  0.40 (   12)
  hydrogen bonds       : bond        0.04413 /  2.83 (  515)
  hydrogen bonds       : angle       4.89093 /  3.61 ( 1488)
  link_BETA1-4         : bond        0.00092 /  0.05 (    1)
  link_BETA1-4         : angle       1.37608 /  0.73 (    3)
  link_NAG-ASN         : bond        0.00352 /  0.19 (    1)
  link_NAG-ASN         : angle       1.36551 /  0.74 (    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
  196 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 195
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  175 TRP cc_start: 0.4656 (t-100) cc_final: 0.3772 (t60)
REVERT: R  184 GLN cc_start: 0.7242 (mm-40) cc_final: 0.6821 (mp10)
REVERT: R  207 MET cc_start: 0.7069 (mtm) cc_final: 0.6749 (ptt)
REVERT: R  308 MET cc_start: 0.5798 (ppp) cc_final: 0.5568 (ppp)
REVERT: R  312 GLN cc_start: 0.8219 (mt0) cc_final: 0.7840 (mt0)
REVERT: A   52 GLN cc_start: 0.7541 (pt0) cc_final: 0.7249 (pt0)
REVERT: A   88 MET cc_start: 0.7842 (ppp) cc_final: 0.7281 (ppp)
REVERT: B   76 ASP cc_start: 0.7418 (p0) cc_final: 0.6961 (p0)
REVERT: B  254 ASP cc_start: 0.7128 (t0) cc_final: 0.6538 (t0)
REVERT: B  331 SER cc_start: 0.8882 (t) cc_final: 0.8439 (m)
REVERT: H  112 TYR cc_start: 0.5647 (m-10) cc_final: 0.4876 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 196
  average time/residue: 0.0990
  time to fit residues: 29.1928
Evaluate side-chains
  147 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 44 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 143 optimal weight:    6.9990
   chunk 81 optimal weight:    6.9990
   chunk 134 optimal weight:    0.0770
   chunk 14 optimal weight:    0.2980
   chunk 10 optimal weight:    0.2980
   chunk 59 optimal weight:    1.9990
   chunk 135 optimal weight:   10.0000
   overall best weight:    0.7140

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  78 ASN
B 156 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 = 0.3897 r_free = 0.3897 target = 0.127267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.108126 restraints weight = 31982.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.106290 restraints weight = 44057.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.107425 restraints weight = 37531.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.107679 restraints weight = 27717.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.107822 restraints weight = 27381.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6691
moved from start:          0.4596

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= 0.120
  Angle     :  0.645  11.735  16430  Z= 0.333
  Chirality :  0.044   0.175   1844
  Planarity :  0.004   0.079   2089
  Dihedral  :  4.616  25.154   1643
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    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: -0.76 (0.21), residues: 1504
  helix:  0.25 (0.22), residues: 519
  sheet: -0.04 (0.32), residues: 279
  loop : -1.23 (0.22), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  70 
 TYR   0.024   0.001   TYR R 178 
 PHE   0.028   0.001   PHE R  91 
 TRP   0.013   0.001   TRP R  35 
 HIS   0.012   0.001   HIS L 199 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.12 (12099)
  covalent geometry    : angle       0.64433 /  0.33 (16412)
  SS BOND              : bond        0.00324 /  0.16 (    6)
  SS BOND              : angle       0.79706 /  0.39 (   12)
  hydrogen bonds       : bond        0.04318 /  2.77 (  515)
  hydrogen bonds       : angle       4.88803 /  3.64 ( 1488)
  link_BETA1-4         : bond        0.00163 /  0.09 (    1)
  link_BETA1-4         : angle       1.45464 /  0.77 (    3)
  link_NAG-ASN         : bond        0.00313 /  0.16 (    1)
  link_NAG-ASN         : angle       1.35521 /  0.73 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1863.24 seconds
wall clock time: 33 minutes 13.05 seconds (1993.05 seconds total)