Starting phenix.real_space_refine
on Wed Mar  4 09:59:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6v03_20968/03_2026/6v03_20968.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6v03_20968/03_2026/6v03_20968.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6v03_20968/03_2026/6v03_20968.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6v03_20968/03_2026/6v03_20968.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6v03_20968/03_2026/6v03_20968.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6v03_20968/03_2026/6v03_20968.map"
  }
  resolution = 3.3
  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=   0.019
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      30      5.16       5
     C    8371      2.51       5
     N    2146      2.21       5
     O    2261      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12808
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 2556
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
      Conformer: "B"
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
          bond proxies already assigned to first conformer: 2513
    Chain: "B"
      Number of atoms: 2553
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
      Conformer: "B"
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
          bond proxies already assigned to first conformer: 2516
    Chain: "C"
      Number of atoms: 2553
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
      Conformer: "B"
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
          bond proxies already assigned to first conformer: 2516
    Chain: "D"
      Number of atoms: 2553
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
      Conformer: "B"
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
          bond proxies already assigned to first conformer: 2516
    Chain: "E"
      Number of atoms: 2553
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
      Conformer: "B"
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
          bond proxies already assigned to first conformer: 2516
    Chain: "A"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 8
          Unusual residues: {'3CN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 8
          Unusual residues: {'3CN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 8
          Unusual residues: {'3CN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 8
          Unusual residues: {'3CN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "E"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 8
          Unusual residues: {'3CN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 11
    residue:
      pdb=" N  ATRP A 160 " occ=0.50
      ... (26 atoms not shown)
      pdb=" CH2BTRP A 160 " occ=0.50
    residue:
      pdb=" N  AHIS A 169 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS A 169 " occ=0.50
    residue:
      pdb=" N  APHE A 282 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 282 " occ=0.50
    residue:
      pdb=" N  AHIS B 169 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS B 169 " occ=0.50
    residue:
      pdb=" N  APHE B 282 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE B 282 " occ=0.50
    residue:
      pdb=" N  AHIS C 169 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS C 169 " occ=0.50
    residue:
      pdb=" N  APHE C 282 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE C 282 " occ=0.50
    residue:
      pdb=" N  AHIS D 169 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS D 169 " occ=0.50
    residue:
      pdb=" N  APHE D 282 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE D 282 " occ=0.50
    residue:
      pdb=" N  AHIS E 169 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS E 169 " occ=0.50
    residue:
      pdb=" N  APHE E 282 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE E 282 " occ=0.50
  Time building chain proxies: 5.24, per 1000 atoms: 0.41
  Number of scatterers: 12808
  At special positions: 0
  Unit cell: (88.7841, 89.8802, 124.955, 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      30     16.00
     O    2261      8.00
     N    2146      7.00
     C    8371      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.10
  Conformation dependent library (CDL) restraints added in 856.2 milliseconds
  

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2960

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 18 sheets defined
      28.6% alpha, 32.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 62
    Processing helix  chain 'A' and resid 63 through 68
      removed outlier: 3.644A  pdb=" N   ASN A  68 " --> pdb=" O   GLU A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 185
    Processing helix  chain 'A' and resid 201 through 204
    Processing helix  chain 'A' and resid 209 through 218
    Processing helix  chain 'A' and resid 219 through 224
      removed outlier: 3.934A  pdb=" N   VAL A 222 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 232
      removed outlier: 4.072A  pdb=" N   LEU A 232 " --> pdb=" O   PHE A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 248
      removed outlier: 3.936A  pdb=" N   LEU A 238 " --> pdb=" O   THR A 234 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   PHE A 247 " --> pdb=" O   VAL A 243 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   TYR A 248 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 285
      removed outlier: 3.956A  pdb=" N   MET A 265 " --> pdb=" O   VAL A 261 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   GLY A 269 " --> pdb=" O   MET A 265 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLY A 271 " --> pdb=" O   ILE A 267 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   SER A 272 " --> pdb=" O   ALA A 268 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ILE A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ALA A 276 " --> pdb=" O   SER A 272 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ILE A 277 " --> pdb=" O   ILE A 273 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N  APHE A 282 " --> pdb=" O   LEU A 278 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ALA A 283 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 299
      removed outlier: 4.019A  pdb=" N   ARG A 299 " --> pdb=" O   LEU A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 316
      removed outlier: 3.914A  pdb=" N   ALA A 310 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ILE A 311 " --> pdb=" O   GLY A 307 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   VAL A 316 " --> pdb=" O   GLY A 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 69
      removed outlier: 3.710A  pdb=" N   ASN B  69 " --> pdb=" O   ARG B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 204
    Processing helix  chain 'B' and resid 209 through 218
    Processing helix  chain 'B' and resid 219 through 224
      removed outlier: 4.004A  pdb=" N   VAL B 222 " --> pdb=" O   SER B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 248
      removed outlier: 4.106A  pdb=" N   GLN B 233 " --> pdb=" O   SER B 229 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU B 240 " --> pdb=" O   PHE B 236 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   THR B 241 " --> pdb=" O   THR B 237 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ALA B 246 " --> pdb=" O   VAL B 242 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   PHE B 247 " --> pdb=" O   VAL B 243 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   TYR B 248 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 282
      removed outlier: 3.511A  pdb=" N   MET B 265 " --> pdb=" O   VAL B 261 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ILE B 273 " --> pdb=" O   GLY B 269 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N  APHE B 282 " --> pdb=" O   LEU B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 317
      removed outlier: 4.177A  pdb=" N   GLY B 312 " --> pdb=" O   PHE B 308 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   CYS B 313 " --> pdb=" O   LEU B 309 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL B 314 " --> pdb=" O   ALA B 310 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   LEU B 315 " --> pdb=" O   ILE B 311 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 61
      No H-bonds generated for 'chain 'C' and resid 59 through 61'
    Processing helix  chain 'C' and resid 62 through 70
      removed outlier: 3.619A  pdb=" N   TRP C  66 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ASN C  68 " --> pdb=" O   GLU C  64 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLY C  70 " --> pdb=" O   TRP C  66 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 153 through 157
      removed outlier: 4.121A  pdb=" N   GLU C 156 " --> pdb=" O   ASP C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 179
      removed outlier: 3.538A  pdb=" N   SER C 179 " --> pdb=" O   ASP C 176 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 176 through 179'
    Processing helix  chain 'C' and resid 209 through 218
    Processing helix  chain 'C' and resid 219 through 224
      removed outlier: 4.011A  pdb=" N   VAL C 222 " --> pdb=" O   SER C 219 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 227 through 248
      removed outlier: 3.671A  pdb=" N   LEU C 232 " --> pdb=" O   PHE C 228 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   GLN C 233 " --> pdb=" O   SER C 229 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   THR C 234 " --> pdb=" O   GLU C 230 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   SER C 235 " --> pdb=" O   ARG C 231 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   PHE C 236 " --> pdb=" O   LEU C 232 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LEU C 240 " --> pdb=" O   PHE C 236 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   THR C 241 " --> pdb=" O   THR C 237 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   PHE C 247 " --> pdb=" O   VAL C 243 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TYR C 248 " --> pdb=" O   ALA C 244 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 260 through 286
      removed outlier: 3.655A  pdb=" N  APHE C 282 " --> pdb=" O   LEU C 278 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 305 through 311
      removed outlier: 3.629A  pdb=" N   LEU C 309 " --> pdb=" O   PRO C 305 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ILE C 311 " --> pdb=" O   GLY C 307 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 70
      removed outlier: 3.568A  pdb=" N   TRP D  66 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ASN D  68 " --> pdb=" O   GLU D  64 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ASN D  69 " --> pdb=" O   ARG D  65 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLY D  70 " --> pdb=" O   TRP D  66 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 201 through 204
    Processing helix  chain 'D' and resid 209 through 218
    Processing helix  chain 'D' and resid 219 through 224
      removed outlier: 3.808A  pdb=" N   VAL D 222 " --> pdb=" O   SER D 219 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 232 through 248
      removed outlier: 3.964A  pdb=" N   LEU D 238 " --> pdb=" O   THR D 234 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   PHE D 247 " --> pdb=" O   VAL D 243 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   TYR D 248 " --> pdb=" O   ALA D 244 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 260 through 282
      removed outlier: 3.626A  pdb=" N   ILE D 273 " --> pdb=" O   GLY D 269 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N  APHE D 282 " --> pdb=" O   LEU D 278 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 302 through 308
      removed outlier: 4.123A  pdb=" N   LEU D 306 " --> pdb=" O   LEU D 302 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   PHE D 308 " --> pdb=" O   PHE D 304 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 308 through 313
      removed outlier: 4.379A  pdb=" N   GLY D 312 " --> pdb=" O   PHE D 308 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   CYS D 313 " --> pdb=" O   LEU D 309 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 308 through 313'
    Processing helix  chain 'E' and resid 62 through 70
      removed outlier: 3.933A  pdb=" N   ASN E  68 " --> pdb=" O   GLU E  64 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ASN E  69 " --> pdb=" O   ARG E  65 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLY E  70 " --> pdb=" O   TRP E  66 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 201 through 204
    Processing helix  chain 'E' and resid 209 through 220
      removed outlier: 3.668A  pdb=" N   ALA E 217 " --> pdb=" O   GLY E 213 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   TRP E 220 " --> pdb=" O   ILE E 216 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 221 through 224
    Processing helix  chain 'E' and resid 227 through 232
      removed outlier: 3.828A  pdb=" N   LEU E 232 " --> pdb=" O   PHE E 228 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 232 through 237
    Processing helix  chain 'E' and resid 238 through 243
      removed outlier: 3.616A  pdb=" N   VAL E 243 " --> pdb=" O   MET E 239 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 243 through 248
      removed outlier: 3.875A  pdb=" N   PHE E 247 " --> pdb=" O   VAL E 243 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   TYR E 248 " --> pdb=" O   ALA E 244 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 243 through 248'
    Processing helix  chain 'E' and resid 260 through 283
    Processing helix  chain 'E' and resid 308 through 313
      removed outlier: 4.322A  pdb=" N   GLY E 312 " --> pdb=" O   PHE E 308 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   CYS E 313 " --> pdb=" O   LEU E 309 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 308 through 313'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58
      removed outlier: 6.366A  pdb=" N   THR A  32 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   GLY A  25 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   LYS A  34 " --> pdb=" O   ILE A  23 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   ILE A  23 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   ASP A  36 " --> pdb=" O   ASN A  21 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   THR A  44 " --> pdb=" O   ASP A  13 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   ASP A  13 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 9.761A  pdb=" N   VAL A  12 " --> pdb=" O   LEU A 140 " (cutoff:3.500A)
      removed outlier: 9.381A  pdb=" N   PHE A 142 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   VAL A  14 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 8.650A  pdb=" N   ASP A 144 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   VAL A  16 " --> pdb=" O   ASP A 144 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   GLN A 146 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ILE A  18 " --> pdb=" O   GLN A 146 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.633A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.633A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 14
    Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 58
      removed outlier: 6.448A  pdb=" N   THR B  32 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   GLY B  25 " --> pdb=" O   THR B  32 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   LYS B  34 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   ILE B  23 " --> pdb=" O   LYS B  34 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   ASP B  36 " --> pdb=" O   ASN B  21 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.600A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.600A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 56 through 58
      removed outlier: 3.567A  pdb=" N   ILE C 101 " --> pdb=" O   MET C  93 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   TYR C  33 " --> pdb=" O   PHE C 110 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   THR C  32 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   GLY C  25 " --> pdb=" O   THR C  32 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   LYS C  34 " --> pdb=" O   ILE C  23 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   ILE C  23 " --> pdb=" O   LYS C  34 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   ASP C  36 " --> pdb=" O   ASN C  21 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   THR C  44 " --> pdb=" O   ASP C  13 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   ASP C  13 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 9.552A  pdb=" N   VAL C  12 " --> pdb=" O   LEU C 140 " (cutoff:3.500A)
      removed outlier: 9.371A  pdb=" N   PHE C 142 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   VAL C  14 " --> pdb=" O   PHE C 142 " (cutoff:3.500A)
      removed outlier: 8.451A  pdb=" N   ASP C 144 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   VAL C  16 " --> pdb=" O   ASP C 144 " (cutoff:3.500A)
      removed outlier: 8.030A  pdb=" N   GLN C 146 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   ILE C  18 " --> pdb=" O   GLN C 146 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.627A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.627A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 56 through 58
      removed outlier: 6.250A  pdb=" N   THR D  32 " --> pdb=" O   GLY D  25 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   GLY D  25 " --> pdb=" O   THR D  32 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   LYS D  34 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   ILE D  23 " --> pdb=" O   LYS D  34 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   ASP D  36 " --> pdb=" O   ASN D  21 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   THR D  44 " --> pdb=" O   ASP D  13 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   ASP D  13 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   VAL D  14 " --> pdb=" O   PHE D 142 " (cutoff:3.500A)
      removed outlier: 8.610A  pdb=" N   ASP D 144 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   VAL D  16 " --> pdb=" O   ASP D 144 " (cutoff:3.500A)
      removed outlier: 8.108A  pdb=" N   GLN D 146 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   ILE D  18 " --> pdb=" O   GLN D 146 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 78
      removed outlier: 4.134A  pdb=" N   ASP D 196 " --> pdb=" O   ARG D 163 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 78
    Processing sheet with id=AB5, first strand: chain 'D' and resid 172 through 174
    Processing sheet with id=AB6, first strand: chain 'E' and resid 13 through 14
    Processing sheet with id=AB7, first strand: chain 'E' and resid 56 through 58
      removed outlier: 6.398A  pdb=" N   THR E  32 " --> pdb=" O   GLY E  25 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   GLY E  25 " --> pdb=" O   THR E  32 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   LYS E  34 " --> pdb=" O   ILE E  23 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   ILE E  23 " --> pdb=" O   LYS E  34 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   ASP E  36 " --> pdb=" O   ASN E  21 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ILE E  18 " --> pdb=" O   GLN E 146 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 78
    Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 78

    476 hydrogen bonds defined for protein.
    1344 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: 1.76

  Time building geometry restraints manager: 1.44 seconds

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

  Histogram of bond lengths:
        1.05 -     1.20: 10
        1.20 -     1.35: 4077
        1.35 -     1.50: 3990
        1.50 -     1.66: 5056
        1.66 -     1.81: 50
  Bond restraints: 13183
  Sorted by residual:
  bond pdb=" CB  3CN B 402 "
       pdb=" CC  3CN B 402 "
    ideal  model  delta    sigma   weight residual
    1.521  1.045  0.476 2.00e-02 2.50e+03 5.66e+02
  bond pdb=" CB  3CN C 402 "
       pdb=" CC  3CN C 402 "
    ideal  model  delta    sigma   weight residual
    1.521  1.045  0.476 2.00e-02 2.50e+03 5.66e+02
  bond pdb=" CB  3CN E 402 "
       pdb=" CC  3CN E 402 "
    ideal  model  delta    sigma   weight residual
    1.521  1.045  0.476 2.00e-02 2.50e+03 5.66e+02
  bond pdb=" CB  3CN A 402 "
       pdb=" CC  3CN A 402 "
    ideal  model  delta    sigma   weight residual
    1.521  1.046  0.475 2.00e-02 2.50e+03 5.64e+02
  bond pdb=" CB  3CN D 402 "
       pdb=" CC  3CN D 402 "
    ideal  model  delta    sigma   weight residual
    1.521  1.046  0.475 2.00e-02 2.50e+03 5.64e+02
  ... (remaining 13178 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 17663
        1.90 -     3.79: 259
        3.79 -     5.69: 35
        5.69 -     7.58: 12
        7.58 -     9.48: 15
  Bond angle restraints: 17984
  Sorted by residual:
  angle pdb=" N   ASN B  60 "
        pdb=" CA  ASN B  60 "
        pdb=" C   ASN B  60 "
      ideal   model   delta    sigma   weight residual
     111.02  115.41   -4.39 1.22e+00 6.72e-01 1.29e+01
  angle pdb=" N   ILE E 209 "
        pdb=" CA  ILE E 209 "
        pdb=" C   ILE E 209 "
      ideal   model   delta    sigma   weight residual
     111.81  108.90    2.91 8.60e-01 1.35e+00 1.14e+01
  angle pdb=" N   ASN A  60 "
        pdb=" CA  ASN A  60 "
        pdb=" C   ASN A  60 "
      ideal   model   delta    sigma   weight residual
     111.02  115.05   -4.03 1.22e+00 6.72e-01 1.09e+01
  angle pdb=" C   GLU B  59 "
        pdb=" N   ASN B  60 "
        pdb=" CA  ASN B  60 "
      ideal   model   delta    sigma   weight residual
     120.79  125.22   -4.43 1.39e+00 5.18e-01 1.01e+01
  angle pdb=" CA  3CN A 402 "
        pdb=" CB  3CN A 402 "
        pdb=" CC  3CN A 402 "
      ideal   model   delta    sigma   weight residual
     112.40  102.98    9.42 3.00e+00 1.11e-01 9.87e+00
  ... (remaining 17979 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 7028
       17.81 -    35.61: 552
       35.61 -    53.42: 114
       53.42 -    71.23: 16
       71.23 -    89.03: 5
  Dihedral angle restraints: 7715
    sinusoidal: 3110
      harmonic: 4605
  Sorted by residual:
  dihedral pdb=" CA  ASN D 137 "
           pdb=" C   ASN D 137 "
           pdb=" N   GLN D 138 "
           pdb=" CA  GLN D 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.84   21.16     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CA  ASN A 137 "
           pdb=" C   ASN A 137 "
           pdb=" N   GLN A 138 "
           pdb=" CA  GLN A 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.24   20.76     0      5.00e+00 4.00e-02 1.72e+01
  dihedral pdb=" CA  LEU A 118 "
           pdb=" C   LEU A 118 "
           pdb=" N   PHE A 119 "
           pdb=" CA  PHE A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.30  -20.70     0      5.00e+00 4.00e-02 1.71e+01
  ... (remaining 7712 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1027
       0.030 -    0.061: 599
       0.061 -    0.091: 203
       0.091 -    0.121: 125
       0.121 -    0.151: 21
  Chirality restraints: 1975
  Sorted by residual:
  chirality pdb=" CA  VAL C 291 "
            pdb=" N   VAL C 291 "
            pdb=" C   VAL C 291 "
            pdb=" CB  VAL C 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.72e-01
  chirality pdb=" CA  ILE C 195 "
            pdb=" N   ILE C 195 "
            pdb=" C   ILE C 195 "
            pdb=" CB  ILE C 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.05e-01
  chirality pdb=" CA  ILE B 195 "
            pdb=" N   ILE B 195 "
            pdb=" C   ILE B 195 "
            pdb=" CB  ILE B 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 1972 not shown)

  Planarity restraints: 2296
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS D  54 "   -0.021 5.00e-02 4.00e+02   3.21e-02 1.64e+00
        pdb=" N   PRO D  55 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO D  55 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO D  55 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  54 "   -0.021 5.00e-02 4.00e+02   3.18e-02 1.61e+00
        pdb=" N   PRO B  55 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO B  55 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B  55 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C  54 "   -0.020 5.00e-02 4.00e+02   2.97e-02 1.41e+00
        pdb=" N   PRO C  55 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO C  55 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C  55 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 2293 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 2230
        2.77 -     3.30: 11614
        3.30 -     3.83: 20058
        3.83 -     4.37: 24706
        4.37 -     4.90: 43125
  Nonbonded interactions: 101733
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 148 "
            pdb=" OD2 ASP B 176 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OD2 ASP D 122 "
            pdb=" NH1 ARG D 199 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" O   GLU B 150 "
            pdb=" ND2 ASN B 154 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" OD1 ASP A 115 "
            pdb=" NH1 ARG A 117 "
     model   vdw
     2.294 3.120
  nonbonded pdb=" O   ARG D 299 "
            pdb=" NH1 ARG D 299 "
     model   vdw
     2.301 3.120
  ... (remaining 101728 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 11 through 64 or resid 66 through 122 or resid 124 through \ 
 159 or resid 161 through 168 or resid 170 through 281 or resid 283 through 402) \ 
)
  selection = (chain 'B' and (resid 11 through 64 or resid 66 through 122 or resid 124 through \ 
 159 or resid 161 through 168 or resid 170 through 281 or resid 283 through 402) \ 
)
  selection = (chain 'C' and (resid 11 through 64 or resid 66 through 122 or resid 124 through \ 
 159 or resid 161 through 168 or resid 170 through 281 or resid 283 through 402) \ 
)
  selection = (chain 'D' and (resid 11 through 64 or resid 66 through 122 or resid 124 through \ 
 159 or resid 161 through 168 or resid 170 through 281 or resid 283 through 402) \ 
)
  selection = (chain 'E' and (resid 11 through 64 or resid 66 through 122 or resid 124 through \ 
 159 or resid 161 through 168 or resid 170 through 281 or resid 283 through 402) \ 
)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.98
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.650
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
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      :  0.014   0.476  13183  Z= 0.677
  Angle     :  0.670   9.480  17984  Z= 0.352
  Chirality :  0.047   0.151   1975
  Planarity :  0.003   0.032   2296
  Dihedral  : 13.488  89.035   4755
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  4.21 %
    Favored  : 95.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -4.30 (0.18), residues: 1572
  helix: -3.03 (0.19), residues: 415
  sheet: -1.93 (0.21), residues: 519
  loop : -3.39 (0.22), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 199 
 TYR   0.007   0.001   TYR A 245 
 PHE   0.017   0.001   PHE D 142 
 TRP   0.013   0.001   TRP B 224 
 HIS   0.006   0.001   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.01364 (13183)
  covalent geometry    : angle       0.66962 (17984)
  hydrogen bonds       : bond        0.15586 (  430)
  hydrogen bonds       : angle       6.86434 ( 1344)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
REVERT: C   86 ASP cc_start: 0.7753 (t70) cc_final: 0.7489 (t70)
REVERT: C  258 TYR cc_start: 0.8712 (p90) cc_final: 0.7962 (p90)
REVERT: D   36 ASP cc_start: 0.8028 (t0) cc_final: 0.7728 (t0)
REVERT: E  216 ILE cc_start: 0.7802 (mm) cc_final: 0.7496 (mt)
REVERT: E  231 ARG cc_start: 0.7194 (mtp-110) cc_final: 0.6965 (mtp85)
REVERT: E  247 PHE cc_start: 0.7463 (t80) cc_final: 0.7228 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.1237
  time to fit residues: 27.7333
Evaluate side-chains
  131 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:   10.0000
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN
A  69 ASN
A  89 ASN
A 124 GLN
A 151 ASN
B  62 GLN
B 124 GLN
B 169 HIS    B
** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  62 GLN
C 284 HIS
D  62 GLN
D 124 GLN
D 138 GLN
D 151 ASN
D 284 HIS
E  60 ASN
E  62 GLN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.173661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.131449 restraints weight = 82308.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 3.93
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3466
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3466 r_free = 0.3466    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3463 r_free = 0.3463    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3463
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.0843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13183  Z= 0.141
  Angle     :  0.576   8.073  17984  Z= 0.294
  Chirality :  0.047   0.156   1975
  Planarity :  0.004   0.038   2296
  Dihedral  :  5.095  28.907   1755
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  8.50 %
    Favored  : 90.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.21 (0.20), residues: 1572
  helix: -2.09 (0.22), residues: 428
  sheet: -1.18 (0.23), residues: 526
  loop : -2.88 (0.23), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 231 
 TYR   0.011   0.001   TYR B 270 
 PHE   0.030   0.001   PHE E 228 
 TRP   0.011   0.001   TRP B 224 
 HIS   0.006   0.001   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (13183)
  covalent geometry    : angle       0.57561 (17984)
  hydrogen bonds       : bond        0.03727 (  430)
  hydrogen bonds       : angle       5.08273 ( 1344)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 156
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
REVERT: C   86 ASP cc_start: 0.7899 (t70) cc_final: 0.7659 (t70)
REVERT: C  247 PHE cc_start: 0.7879 (t80) cc_final: 0.7561 (t80)
REVERT: C  258 TYR cc_start: 0.8688 (p90) cc_final: 0.8005 (p90)
REVERT: E  216 ILE cc_start: 0.7970 (mm) cc_final: 0.7703 (mt)
REVERT: E  247 PHE cc_start: 0.7854 (t80) cc_final: 0.7633 (t80)
  outliers start: 8
  outliers final: 4
  residues processed: 159
  average time/residue: 0.1079
  time to fit residues: 25.3429
Evaluate side-chains
  145 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 141
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain D residue  138 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 129 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 117 optimal weight:    5.9990
   chunk 149 optimal weight:    9.9990
   chunk 76 optimal weight:    4.9990
   chunk 97 optimal weight:    4.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A  89 ASN
B 287 GLN
C 284 HIS
E  69 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.172487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.128502 restraints weight = 66694.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 4.03
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3420
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3420 r_free = 0.3420    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3420 r_free = 0.3420    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3420
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.1054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  13183  Z= 0.180
  Angle     :  0.592   7.516  17984  Z= 0.304
  Chirality :  0.048   0.152   1975
  Planarity :  0.004   0.033   2296
  Dihedral  :  5.116  26.416   1755
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 11.07 %
    Favored  : 87.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.72 (0.21), residues: 1572
  helix: -1.74 (0.24), residues: 430
  sheet: -0.79 (0.23), residues: 519
  loop : -2.64 (0.23), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 190 
 TYR   0.008   0.001   TYR B 148 
 PHE   0.019   0.001   PHE D 228 
 TRP   0.010   0.001   TRP A  43 
 HIS   0.008   0.002   HIS A 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 (13183)
  covalent geometry    : angle       0.59178 (17984)
  hydrogen bonds       : bond        0.03507 (  430)
  hydrogen bonds       : angle       4.87105 ( 1344)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 139
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
REVERT: C   86 ASP cc_start: 0.7929 (t70) cc_final: 0.7697 (t70)
REVERT: C  258 TYR cc_start: 0.8705 (p90) cc_final: 0.8011 (p90)
REVERT: E  216 ILE cc_start: 0.7955 (mm) cc_final: 0.7700 (mt)
REVERT: E  247 PHE cc_start: 0.7823 (t80) cc_final: 0.7596 (t80)
  outliers start: 11
  outliers final: 7
  residues processed: 143
  average time/residue: 0.1150
  time to fit residues: 24.1879
Evaluate side-chains
  140 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 133
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain B residue  241 THR
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain E residue  196 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 53 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 136 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0470
   chunk 105 optimal weight:    0.9990
   chunk 91 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 81 optimal weight:    9.9990
   overall best weight:    1.6086

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

Flipped N/Q/H residues before XYZ refinement:
B 138 GLN
C 284 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.172397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.127821 restraints weight = 82518.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 4.32
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3427
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3427 r_free = 0.3427    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3427 r_free = 0.3427    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3427
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.1217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  13183  Z= 0.152
  Angle     :  0.571   7.699  17984  Z= 0.291
  Chirality :  0.047   0.150   1975
  Planarity :  0.003   0.032   2296
  Dihedral  :  4.953  23.580   1755
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 11.79 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.36 (0.21), residues: 1572
  helix: -1.53 (0.24), residues: 430
  sheet: -0.54 (0.24), residues: 520
  loop : -2.40 (0.24), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 190 
 TYR   0.008   0.001   TYR C  38 
 PHE   0.017   0.001   PHE D 228 
 TRP   0.010   0.001   TRP B 224 
 HIS   0.008   0.002   HIS A 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (13183)
  covalent geometry    : angle       0.57058 (17984)
  hydrogen bonds       : bond        0.03299 (  430)
  hydrogen bonds       : angle       4.70678 ( 1344)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 146
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
REVERT: B   39 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8337 (tt)
REVERT: B  159 GLU cc_start: 0.7245 (tt0) cc_final: 0.6997 (tp30)
REVERT: C   86 ASP cc_start: 0.7951 (t70) cc_final: 0.7729 (t70)
REVERT: C  258 TYR cc_start: 0.8669 (p90) cc_final: 0.7968 (p90)
REVERT: D  258 TYR cc_start: 0.8466 (p90) cc_final: 0.7958 (p90)
REVERT: E  216 ILE cc_start: 0.7807 (mm) cc_final: 0.7531 (mt)
REVERT: E  247 PHE cc_start: 0.7786 (t80) cc_final: 0.7586 (t80)
  outliers start: 16
  outliers final: 13
  residues processed: 154
  average time/residue: 0.1071
  time to fit residues: 24.9710
Evaluate side-chains
  149 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  141 ARG
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  138 GLN
Chi-restraints excluded: chain B residue  241 THR
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain D residue   15 SER
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  196 ASP
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain E residue  196 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 11 optimal weight:    0.0870
   chunk 117 optimal weight:    0.0980
   chunk 29 optimal weight:    8.9990
   chunk 31 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 122 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 21 optimal weight:    9.9990
   chunk 133 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    1.2364

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

Flipped N/Q/H residues before XYZ refinement:
C 124 GLN
C 284 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.173996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.130241 restraints weight = 76185.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 4.21
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3449
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|
r_final: 0.3449
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.1364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  13183  Z= 0.130
  Angle     :  0.550   7.610  17984  Z= 0.280
  Chirality :  0.047   0.171   1975
  Planarity :  0.003   0.031   2296
  Dihedral  :  4.784  20.802   1755
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.57 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.99 (0.21), residues: 1572
  helix: -1.22 (0.25), residues: 425
  sheet: -0.35 (0.24), residues: 520
  loop : -2.16 (0.24), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 255 
 TYR   0.008   0.001   TYR A  38 
 PHE   0.039   0.001   PHE A 228 
 TRP   0.009   0.001   TRP B 224 
 HIS   0.008   0.002   HIS A 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (13183)
  covalent geometry    : angle       0.55016 (17984)
  hydrogen bonds       : bond        0.03160 (  430)
  hydrogen bonds       : angle       4.54707 ( 1344)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
REVERT: B   39 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8288 (tt)
REVERT: B  159 GLU cc_start: 0.7199 (tt0) cc_final: 0.6982 (tp30)
REVERT: C   86 ASP cc_start: 0.7949 (t70) cc_final: 0.7716 (t70)
REVERT: C  258 TYR cc_start: 0.8669 (p90) cc_final: 0.7952 (p90)
REVERT: D  203 TYR cc_start: 0.9138 (t80) cc_final: 0.8915 (t80)
REVERT: D  258 TYR cc_start: 0.8420 (p90) cc_final: 0.7892 (p90)
  outliers start: 14
  outliers final: 10
  residues processed: 160
  average time/residue: 0.1050
  time to fit residues: 25.3712
Evaluate side-chains
  152 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 141
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  141 ARG
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain C residue  202 SER
Chi-restraints excluded: chain D residue   15 SER
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain E residue  196 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 52 optimal weight:    9.9990
   chunk 46 optimal weight:    4.9990
   chunk 92 optimal weight:    0.7980
   chunk 97 optimal weight:    6.9990
   chunk 106 optimal weight:    2.9990
   chunk 78 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 125 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0040
   chunk 23 optimal weight:    6.9990
   chunk 11 optimal weight:    0.4980
   overall best weight:    1.0596

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
C 284 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.174747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.130471 restraints weight = 74947.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 4.15
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3449
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|
r_final: 0.3449
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  13183  Z= 0.118
  Angle     :  0.539   7.703  17984  Z= 0.273
  Chirality :  0.046   0.173   1975
  Planarity :  0.003   0.030   2296
  Dihedral  :  4.600  18.514   1755
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 13.29 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.63 (0.22), residues: 1572
  helix: -0.88 (0.26), residues: 411
  sheet: -0.14 (0.24), residues: 515
  loop : -1.95 (0.24), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 255 
 TYR   0.008   0.001   TYR C  38 
 PHE   0.034   0.001   PHE A 228 
 TRP   0.009   0.001   TRP D 206 
 HIS   0.008   0.002   HIS A 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (13183)
  covalent geometry    : angle       0.53939 (17984)
  hydrogen bonds       : bond        0.03026 (  430)
  hydrogen bonds       : angle       4.41502 ( 1344)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
REVERT: B  159 GLU cc_start: 0.7222 (tt0) cc_final: 0.6983 (tp30)
REVERT: C  247 PHE cc_start: 0.7778 (t80) cc_final: 0.7471 (t80)
REVERT: C  258 TYR cc_start: 0.8683 (p90) cc_final: 0.7962 (p90)
REVERT: D  203 TYR cc_start: 0.9139 (t80) cc_final: 0.8852 (t80)
REVERT: D  258 TYR cc_start: 0.8359 (p90) cc_final: 0.7834 (p90)
  outliers start: 16
  outliers final: 12
  residues processed: 165
  average time/residue: 0.1074
  time to fit residues: 26.3667
Evaluate side-chains
  161 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 149
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  138 GLN
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain B residue  241 THR
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain C residue  202 SER
Chi-restraints excluded: chain D residue   15 SER
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  196 ASP
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  147 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 149 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 120 optimal weight:    0.7980
   chunk 124 optimal weight:    0.8980
   chunk 122 optimal weight:    0.8980
   chunk 146 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 138 GLN
C  60 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.175838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.120342 restraints weight = 76953.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 5.73
r_work: 0.3110 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3105
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3105
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  13183  Z= 0.110
  Angle     :  0.532   7.661  17984  Z= 0.270
  Chirality :  0.046   0.211   1975
  Planarity :  0.003   0.030   2296
  Dihedral  :  4.502  17.817   1755
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.64 %
    Favored  : 84.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.43 (0.22), residues: 1572
  helix: -0.75 (0.26), residues: 411
  sheet:  0.03 (0.25), residues: 515
  loop : -1.84 (0.25), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 255 
 TYR   0.008   0.001   TYR C  38 
 PHE   0.013   0.001   PHE D 228 
 TRP   0.009   0.001   TRP D 206 
 HIS   0.009   0.002   HIS A 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (13183)
  covalent geometry    : angle       0.53231 (17984)
  hydrogen bonds       : bond        0.02987 (  430)
  hydrogen bonds       : angle       4.34613 ( 1344)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
REVERT: B  159 GLU cc_start: 0.7441 (tt0) cc_final: 0.6798 (tp30)
REVERT: C  247 PHE cc_start: 0.7371 (t80) cc_final: 0.7025 (t80)
REVERT: C  258 TYR cc_start: 0.8831 (p90) cc_final: 0.7860 (p90)
REVERT: D  258 TYR cc_start: 0.8411 (p90) cc_final: 0.7651 (p90)
  outliers start: 14
  outliers final: 13
  residues processed: 157
  average time/residue: 0.1027
  time to fit residues: 24.1198
Evaluate side-chains
  159 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 146
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain B residue  138 GLN
Chi-restraints excluded: chain B residue  241 THR
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain C residue  202 SER
Chi-restraints excluded: chain D residue   15 SER
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  196 ASP
Chi-restraints excluded: chain D residue  245 TYR
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  147 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 108 optimal weight:    0.9980
   chunk 121 optimal weight:    2.9990
   chunk 113 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 138 GLN
C  60 ASN
C 284 HIS
D 233 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.172300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.128144 restraints weight = 67476.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 4.03
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3407
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3407 r_free = 0.3407    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3407 r_free = 0.3407    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3407
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.1562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  13183  Z= 0.193
  Angle     :  0.594   7.273  17984  Z= 0.304
  Chirality :  0.048   0.216   1975
  Planarity :  0.004   0.032   2296
  Dihedral  :  4.861  21.450   1755
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 13.93 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.55 (0.22), residues: 1572
  helix: -0.82 (0.26), residues: 419
  sheet: -0.01 (0.25), residues: 511
  loop : -1.96 (0.24), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 190 
 TYR   0.009   0.001   TYR A 148 
 PHE   0.013   0.001   PHE C 106 
 TRP   0.010   0.001   TRP D 206 
 HIS   0.008   0.002   HIS A 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 (13183)
  covalent geometry    : angle       0.59367 (17984)
  hydrogen bonds       : bond        0.03234 (  430)
  hydrogen bonds       : angle       4.63274 ( 1344)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
REVERT: C  258 TYR cc_start: 0.8692 (p90) cc_final: 0.7997 (p90)
REVERT: D  258 TYR cc_start: 0.8344 (p90) cc_final: 0.7824 (p90)
REVERT: E  216 ILE cc_start: 0.7767 (mm) cc_final: 0.7506 (mt)
  outliers start: 16
  outliers final: 15
  residues processed: 152
  average time/residue: 0.1174
  time to fit residues: 26.0345
Evaluate side-chains
  153 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  138 GLN
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  202 SER
Chi-restraints excluded: chain D residue   15 SER
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  196 ASP
Chi-restraints excluded: chain D residue  245 TYR
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  147 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 101 optimal weight:    0.9980
   chunk 14 optimal weight:    8.9990
   chunk 142 optimal weight:    9.9990
   chunk 137 optimal weight:    0.7980
   chunk 74 optimal weight:    8.9990
   chunk 108 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 114 optimal weight:    6.9990
   chunk 147 optimal weight:    7.9990
   chunk 116 optimal weight:    2.9990
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 ASN
B 138 GLN
C 284 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.171792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.124534 restraints weight = 75660.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 4.38
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3370
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3370 r_free = 0.3370    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3369 r_free = 0.3369    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|
r_final: 0.3369
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.110  13183  Z= 0.199
  Angle     :  0.931  59.199  17984  Z= 0.546
  Chirality :  0.049   0.405   1975
  Planarity :  0.005   0.137   2296
  Dihedral  :  4.879  22.199   1755
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.66 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.93 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.54 (0.22), residues: 1572
  helix: -0.81 (0.26), residues: 419
  sheet: -0.00 (0.25), residues: 511
  loop : -1.95 (0.24), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 190 
 TYR   0.008   0.001   TYR B 148 
 PHE   0.012   0.001   PHE C 106 
 TRP   0.009   0.001   TRP D 206 
 HIS   0.008   0.002   HIS A 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 (13183)
  covalent geometry    : angle       0.93138 (17984)
  hydrogen bonds       : bond        0.03229 (  430)
  hydrogen bonds       : angle       4.62847 ( 1344)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 138
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
REVERT: C  258 TYR cc_start: 0.8737 (p90) cc_final: 0.7932 (p90)
REVERT: D  258 TYR cc_start: 0.8358 (p90) cc_final: 0.7761 (p90)
REVERT: E  216 ILE cc_start: 0.7625 (mm) cc_final: 0.7368 (mt)
  outliers start: 14
  outliers final: 13
  residues processed: 149
  average time/residue: 0.1128
  time to fit residues: 24.8464
Evaluate side-chains
  150 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 137
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  202 SER
Chi-restraints excluded: chain D residue   15 SER
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  196 ASP
Chi-restraints excluded: chain D residue  245 TYR
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  147 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 55 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 122 optimal weight:    2.9990
   chunk 103 optimal weight:    0.6980
   chunk 134 optimal weight:    2.9990
   chunk 58 optimal weight:    9.9990
   chunk 146 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 82 optimal weight:    4.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 138 GLN
C 284 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.172455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.127970 restraints weight = 73161.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 4.13
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3423
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3423 r_free = 0.3423    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3423 r_free = 0.3423    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|
r_final: 0.3423
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.110  13183  Z= 0.199
  Angle     :  0.931  59.199  17984  Z= 0.546
  Chirality :  0.049   0.405   1975
  Planarity :  0.005   0.137   2296
  Dihedral  :  4.879  22.199   1755
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.66 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 14.07 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.54 (0.22), residues: 1572
  helix: -0.81 (0.26), residues: 419
  sheet: -0.00 (0.25), residues: 511
  loop : -1.95 (0.24), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 190 
 TYR   0.008   0.001   TYR B 148 
 PHE   0.012   0.001   PHE C 106 
 TRP   0.009   0.001   TRP D 206 
 HIS   0.008   0.002   HIS A 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 (13183)
  covalent geometry    : angle       0.93138 (17984)
  hydrogen bonds       : bond        0.03229 (  430)
  hydrogen bonds       : angle       4.62847 ( 1344)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 137
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: C  258 TYR cc_start: 0.8696 (p90) cc_final: 0.7987 (p90)
REVERT: D  258 TYR cc_start: 0.8347 (p90) cc_final: 0.7822 (p90)
REVERT: E  216 ILE cc_start: 0.7759 (mm) cc_final: 0.7500 (mt)
  outliers start: 14
  outliers final: 13
  residues processed: 148
  average time/residue: 0.1145
  time to fit residues: 24.8756
Evaluate side-chains
  150 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 137
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  202 SER
Chi-restraints excluded: chain D residue   15 SER
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  196 ASP
Chi-restraints excluded: chain D residue  245 TYR
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  147 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 58 optimal weight:   20.0000
   chunk 24 optimal weight:    0.6980
   chunk 140 optimal weight:    3.9990
   chunk 123 optimal weight:    0.0980
   chunk 53 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 134 optimal weight:    6.9990
   chunk 85 optimal weight:    2.9990
   chunk 128 optimal weight:    0.9990
   chunk 60 optimal weight:    4.9990
   chunk 59 optimal weight:    7.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 138 GLN
C 284 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.172534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.128698 restraints weight = 77700.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 4.23
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3430
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3430 r_free = 0.3430    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3430 r_free = 0.3430    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|
r_final: 0.3430
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.110  13183  Z= 0.199
  Angle     :  0.931  59.199  17984  Z= 0.546
  Chirality :  0.049   0.405   1975
  Planarity :  0.005   0.137   2296
  Dihedral  :  4.879  22.199   1755
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.66 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 14.07 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.54 (0.22), residues: 1572
  helix: -0.81 (0.26), residues: 419
  sheet: -0.00 (0.25), residues: 511
  loop : -1.95 (0.24), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 190 
 TYR   0.008   0.001   TYR B 148 
 PHE   0.012   0.001   PHE C 106 
 TRP   0.009   0.001   TRP D 206 
 HIS   0.008   0.002   HIS A 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 (13183)
  covalent geometry    : angle       0.93138 (17984)
  hydrogen bonds       : bond        0.03229 (  430)
  hydrogen bonds       : angle       4.62847 ( 1344)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2314.82 seconds
wall clock time: 40 minutes 33.74 seconds (2433.74 seconds total)