Starting phenix.real_space_refine
on Sat Sep 12 03:13:25 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6cju_7484/09_2026/6cju_7484.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6cju_7484/09_2026/6cju_7484.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.35
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/6cju_7484/09_2026/6cju_7484.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6cju_7484/09_2026/6cju_7484.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6cju_7484/09_2026/6cju_7484.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6cju_7484/09_2026/6cju_7484.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6cju_7484/09_2026/6cju_7484.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6cju_7484/09_2026/6cju_7484.cif"
  }
  resolution = 3.35
  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=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     S      28      5.16       5
     C    8704      2.51       5
     N    2080      2.21       5
     O    2256      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13076
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 390, 3102
          Classifications: {'peptide': 390}
          Link IDs: {'PTRANS': 24, 'TRANS': 365}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 167
          Unusual residues: {'PGW': 8}
          Classifications: {'RNAv2': 1, 'undetermined': 8}
          Modifications used: {'rna3p': 1}
          Link IDs: {None: 8}
          Unresolved non-hydrogen bonds: 263
          Unresolved non-hydrogen angles: 309
          Unresolved non-hydrogen dihedrals: 178
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'PGW:plan-1': 6, 'PGW:plan-2': 6, 'PGW:plan-3': 7}
          Unresolved non-hydrogen planarities: 61
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 3.07, per 1000 atoms: 0.23
  Number of scatterers: 13076
  At special positions: 0
  Unit cell: (106.252, 106.252, 120.204, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      28     16.00
     P       8     15.00
     O    2256      8.00
     N    2080      7.00
     C    8704      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: 1.05
  Conformation dependent library (CDL) restraints added in 574.3 milliseconds
  

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 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:
      76 helices and 0 sheets defined
      66.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 35
      removed outlier: 4.436A  pdb=" N   VAL A  14 " --> pdb=" O   THR A  10 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   TRP A  15 " --> pdb=" O   TYR A  11 " (cutoff:3.500A)
      Proline residue:  A  31  - end of helix
      removed outlier: 3.760A  pdb=" N   VAL A  35 " --> pdb=" O   PRO A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 62
      removed outlier: 6.360A  pdb=" N   LEU A  43 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      Proline residue:  A  45  - end of helix
      removed outlier: 4.324A  pdb=" N   ILE A  58 " --> pdb=" O   LEU A  54 " (cutoff:3.500A)
      Proline residue:  A  59  - end of helix
    Processing helix  chain 'A' and resid 82 through 88
    Processing helix  chain 'A' and resid 91 through 98
      removed outlier: 4.697A  pdb=" N   VAL A  95 " --> pdb=" O   LEU A  91 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   PHE A  96 " --> pdb=" O   ASP A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 104
      No H-bonds generated for 'chain 'A' and resid 103 through 104'
    Processing helix  chain 'A' and resid 105 through 114
      removed outlier: 4.091A  pdb=" N   ARG A 111 " --> pdb=" O   SER A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 126
      removed outlier: 4.057A  pdb=" N   ARG A 124 " --> pdb=" O   ARG A 120 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   LEU A 126 " --> pdb=" O   ALA A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 158
      removed outlier: 3.535A  pdb=" N   ARG A 136 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   GLY A 150 " --> pdb=" O   LEU A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 181
      removed outlier: 4.040A  pdb=" N   TYR A 170 " --> pdb=" O   ALA A 166 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   SER A 172 " --> pdb=" O   THR A 168 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ALA A 173 " --> pdb=" O   ARG A 169 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LEU A 181 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 224
      removed outlier: 3.811A  pdb=" N   TYR A 199 " --> pdb=" O   THR A 195 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   LYS A 224 " --> pdb=" O   SER A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 245
      removed outlier: 3.862A  pdb=" N   ARG A 233 " --> pdb=" O   LYS A 229 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   VAL A 239 " --> pdb=" O   ARG A 235 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   THR A 240 " --> pdb=" O   VAL A 236 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   TYR A 245 " --> pdb=" O   ALA A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 267
      removed outlier: 3.767A  pdb=" N   ARG A 267 " --> pdb=" O   LEU A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 278
      removed outlier: 3.707A  pdb=" N   LEU A 276 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   LYS A 277 " --> pdb=" O   ARG A 273 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   GLU A 278 " --> pdb=" O   GLU A 274 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 272 through 278'
    Processing helix  chain 'A' and resid 281 through 292
    Processing helix  chain 'A' and resid 293 through 298
      removed outlier: 4.031A  pdb=" N   GLU A 297 " --> pdb=" O   GLY A 293 " (cutoff:3.500A)
      removed outlier: 5.678A  pdb=" N   LYS A 298 " --> pdb=" O   ASP A 294 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 293 through 298'
    Processing helix  chain 'A' and resid 307 through 316
      removed outlier: 3.637A  pdb=" N   ARG A 311 " --> pdb=" O   GLU A 307 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ASP A 312 " --> pdb=" O   GLU A 308 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   LEU A 315 " --> pdb=" O   ARG A 311 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   HIS A 316 " --> pdb=" O   ASP A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 373
      removed outlier: 4.574A  pdb=" N   ILE A 372 " --> pdb=" O   GLU A 368 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   LEU A 373 " --> pdb=" O   MET A 369 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 368 through 373'
    Processing helix  chain 'A' and resid 394 through 403
      removed outlier: 3.592A  pdb=" N   SER A 402 " --> pdb=" O   ASP A 398 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ARG A 403 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 412
      removed outlier: 4.348A  pdb=" N   GLN A 412 " --> pdb=" O   ALA A 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 35
      removed outlier: 4.436A  pdb=" N   VAL B  14 " --> pdb=" O   THR B  10 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   TRP B  15 " --> pdb=" O   TYR B  11 " (cutoff:3.500A)
      Proline residue:  B  31  - end of helix
      removed outlier: 3.760A  pdb=" N   VAL B  35 " --> pdb=" O   PRO B  31 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 39 through 62
      removed outlier: 6.360A  pdb=" N   LEU B  43 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
      Proline residue:  B  45  - end of helix
      removed outlier: 4.324A  pdb=" N   ILE B  58 " --> pdb=" O   LEU B  54 " (cutoff:3.500A)
      Proline residue:  B  59  - end of helix
    Processing helix  chain 'B' and resid 82 through 88
    Processing helix  chain 'B' and resid 91 through 98
      removed outlier: 4.697A  pdb=" N   VAL B  95 " --> pdb=" O   LEU B  91 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   PHE B  96 " --> pdb=" O   ASP B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 104
      No H-bonds generated for 'chain 'B' and resid 103 through 104'
    Processing helix  chain 'B' and resid 105 through 114
      removed outlier: 4.091A  pdb=" N   ARG B 111 " --> pdb=" O   SER B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 126
      removed outlier: 4.057A  pdb=" N   ARG B 124 " --> pdb=" O   ARG B 120 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   LEU B 126 " --> pdb=" O   ALA B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 158
      removed outlier: 3.535A  pdb=" N   ARG B 136 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   GLY B 150 " --> pdb=" O   LEU B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 181
      removed outlier: 4.040A  pdb=" N   TYR B 170 " --> pdb=" O   ALA B 166 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   SER B 172 " --> pdb=" O   THR B 168 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ALA B 173 " --> pdb=" O   ARG B 169 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LEU B 181 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 224
      removed outlier: 3.811A  pdb=" N   TYR B 199 " --> pdb=" O   THR B 195 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   LYS B 224 " --> pdb=" O   SER B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 245
      removed outlier: 3.862A  pdb=" N   ARG B 233 " --> pdb=" O   LYS B 229 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   VAL B 239 " --> pdb=" O   ARG B 235 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   THR B 240 " --> pdb=" O   VAL B 236 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   TYR B 245 " --> pdb=" O   ALA B 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 267
      removed outlier: 3.767A  pdb=" N   ARG B 267 " --> pdb=" O   LEU B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 278
      removed outlier: 3.707A  pdb=" N   LEU B 276 " --> pdb=" O   GLU B 272 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   LYS B 277 " --> pdb=" O   ARG B 273 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   GLU B 278 " --> pdb=" O   GLU B 274 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 272 through 278'
    Processing helix  chain 'B' and resid 281 through 292
    Processing helix  chain 'B' and resid 293 through 298
      removed outlier: 4.031A  pdb=" N   GLU B 297 " --> pdb=" O   GLY B 293 " (cutoff:3.500A)
      removed outlier: 5.678A  pdb=" N   LYS B 298 " --> pdb=" O   ASP B 294 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 293 through 298'
    Processing helix  chain 'B' and resid 307 through 316
      removed outlier: 3.637A  pdb=" N   ARG B 311 " --> pdb=" O   GLU B 307 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ASP B 312 " --> pdb=" O   GLU B 308 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   LEU B 315 " --> pdb=" O   ARG B 311 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   HIS B 316 " --> pdb=" O   ASP B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 373
      removed outlier: 4.574A  pdb=" N   ILE B 372 " --> pdb=" O   GLU B 368 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   LEU B 373 " --> pdb=" O   MET B 369 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 368 through 373'
    Processing helix  chain 'B' and resid 394 through 403
      removed outlier: 3.592A  pdb=" N   SER B 402 " --> pdb=" O   ASP B 398 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ARG B 403 " --> pdb=" O   ARG B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 412
      removed outlier: 4.348A  pdb=" N   GLN B 412 " --> pdb=" O   ALA B 408 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 35
      removed outlier: 4.436A  pdb=" N   VAL C  14 " --> pdb=" O   THR C  10 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   TRP C  15 " --> pdb=" O   TYR C  11 " (cutoff:3.500A)
      Proline residue:  C  31  - end of helix
      removed outlier: 3.760A  pdb=" N   VAL C  35 " --> pdb=" O   PRO C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 39 through 62
      removed outlier: 6.360A  pdb=" N   LEU C  43 " --> pdb=" O   LEU C  39 " (cutoff:3.500A)
      Proline residue:  C  45  - end of helix
      removed outlier: 4.324A  pdb=" N   ILE C  58 " --> pdb=" O   LEU C  54 " (cutoff:3.500A)
      Proline residue:  C  59  - end of helix
    Processing helix  chain 'C' and resid 82 through 88
    Processing helix  chain 'C' and resid 91 through 98
      removed outlier: 4.697A  pdb=" N   VAL C  95 " --> pdb=" O   LEU C  91 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   PHE C  96 " --> pdb=" O   ASP C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 104
      No H-bonds generated for 'chain 'C' and resid 103 through 104'
    Processing helix  chain 'C' and resid 105 through 114
      removed outlier: 4.091A  pdb=" N   ARG C 111 " --> pdb=" O   SER C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 126
      removed outlier: 4.057A  pdb=" N   ARG C 124 " --> pdb=" O   ARG C 120 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   LEU C 126 " --> pdb=" O   ALA C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 158
      removed outlier: 3.535A  pdb=" N   ARG C 136 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   GLY C 150 " --> pdb=" O   LEU C 146 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 166 through 181
      removed outlier: 4.040A  pdb=" N   TYR C 170 " --> pdb=" O   ALA C 166 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   SER C 172 " --> pdb=" O   THR C 168 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ALA C 173 " --> pdb=" O   ARG C 169 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LEU C 181 " --> pdb=" O   THR C 177 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 194 through 224
      removed outlier: 3.811A  pdb=" N   TYR C 199 " --> pdb=" O   THR C 195 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   LYS C 224 " --> pdb=" O   SER C 220 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 227 through 245
      removed outlier: 3.862A  pdb=" N   ARG C 233 " --> pdb=" O   LYS C 229 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   VAL C 239 " --> pdb=" O   ARG C 235 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   THR C 240 " --> pdb=" O   VAL C 236 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   TYR C 245 " --> pdb=" O   ALA C 241 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 267
      removed outlier: 3.767A  pdb=" N   ARG C 267 " --> pdb=" O   LEU C 263 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 272 through 278
      removed outlier: 3.707A  pdb=" N   LEU C 276 " --> pdb=" O   GLU C 272 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   LYS C 277 " --> pdb=" O   ARG C 273 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   GLU C 278 " --> pdb=" O   GLU C 274 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 272 through 278'
    Processing helix  chain 'C' and resid 281 through 292
    Processing helix  chain 'C' and resid 293 through 298
      removed outlier: 4.031A  pdb=" N   GLU C 297 " --> pdb=" O   GLY C 293 " (cutoff:3.500A)
      removed outlier: 5.678A  pdb=" N   LYS C 298 " --> pdb=" O   ASP C 294 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 293 through 298'
    Processing helix  chain 'C' and resid 307 through 316
      removed outlier: 3.637A  pdb=" N   ARG C 311 " --> pdb=" O   GLU C 307 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ASP C 312 " --> pdb=" O   GLU C 308 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   LEU C 315 " --> pdb=" O   ARG C 311 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   HIS C 316 " --> pdb=" O   ASP C 312 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 368 through 373
      removed outlier: 4.574A  pdb=" N   ILE C 372 " --> pdb=" O   GLU C 368 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   LEU C 373 " --> pdb=" O   MET C 369 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 368 through 373'
    Processing helix  chain 'C' and resid 394 through 403
      removed outlier: 3.592A  pdb=" N   SER C 402 " --> pdb=" O   ASP C 398 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ARG C 403 " --> pdb=" O   ARG C 399 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 412
      removed outlier: 4.348A  pdb=" N   GLN C 412 " --> pdb=" O   ALA C 408 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 10 through 35
      removed outlier: 4.436A  pdb=" N   VAL D  14 " --> pdb=" O   THR D  10 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   TRP D  15 " --> pdb=" O   TYR D  11 " (cutoff:3.500A)
      Proline residue:  D  31  - end of helix
      removed outlier: 3.760A  pdb=" N   VAL D  35 " --> pdb=" O   PRO D  31 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 39 through 62
      removed outlier: 6.360A  pdb=" N   LEU D  43 " --> pdb=" O   LEU D  39 " (cutoff:3.500A)
      Proline residue:  D  45  - end of helix
      removed outlier: 4.324A  pdb=" N   ILE D  58 " --> pdb=" O   LEU D  54 " (cutoff:3.500A)
      Proline residue:  D  59  - end of helix
    Processing helix  chain 'D' and resid 82 through 88
    Processing helix  chain 'D' and resid 91 through 98
      removed outlier: 4.697A  pdb=" N   VAL D  95 " --> pdb=" O   LEU D  91 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   PHE D  96 " --> pdb=" O   ASP D  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 104
      No H-bonds generated for 'chain 'D' and resid 103 through 104'
    Processing helix  chain 'D' and resid 105 through 114
      removed outlier: 4.091A  pdb=" N   ARG D 111 " --> pdb=" O   SER D 108 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 115 through 126
      removed outlier: 4.057A  pdb=" N   ARG D 124 " --> pdb=" O   ARG D 120 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   LEU D 126 " --> pdb=" O   ALA D 122 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 132 through 158
      removed outlier: 3.535A  pdb=" N   ARG D 136 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   GLY D 150 " --> pdb=" O   LEU D 146 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 166 through 181
      removed outlier: 4.040A  pdb=" N   TYR D 170 " --> pdb=" O   ALA D 166 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   SER D 172 " --> pdb=" O   THR D 168 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ALA D 173 " --> pdb=" O   ARG D 169 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LEU D 181 " --> pdb=" O   THR D 177 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 194 through 224
      removed outlier: 3.811A  pdb=" N   TYR D 199 " --> pdb=" O   THR D 195 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   LYS D 224 " --> pdb=" O   SER D 220 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 227 through 245
      removed outlier: 3.862A  pdb=" N   ARG D 233 " --> pdb=" O   LYS D 229 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   VAL D 239 " --> pdb=" O   ARG D 235 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   THR D 240 " --> pdb=" O   VAL D 236 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   TYR D 245 " --> pdb=" O   ALA D 241 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 250 through 267
      removed outlier: 3.767A  pdb=" N   ARG D 267 " --> pdb=" O   LEU D 263 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 272 through 278
      removed outlier: 3.707A  pdb=" N   LEU D 276 " --> pdb=" O   GLU D 272 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   LYS D 277 " --> pdb=" O   ARG D 273 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   GLU D 278 " --> pdb=" O   GLU D 274 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 272 through 278'
    Processing helix  chain 'D' and resid 281 through 292
    Processing helix  chain 'D' and resid 293 through 298
      removed outlier: 4.031A  pdb=" N   GLU D 297 " --> pdb=" O   GLY D 293 " (cutoff:3.500A)
      removed outlier: 5.678A  pdb=" N   LYS D 298 " --> pdb=" O   ASP D 294 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 293 through 298'
    Processing helix  chain 'D' and resid 307 through 316
      removed outlier: 3.637A  pdb=" N   ARG D 311 " --> pdb=" O   GLU D 307 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ASP D 312 " --> pdb=" O   GLU D 308 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   LEU D 315 " --> pdb=" O   ARG D 311 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   HIS D 316 " --> pdb=" O   ASP D 312 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 368 through 373
      removed outlier: 4.574A  pdb=" N   ILE D 372 " --> pdb=" O   GLU D 368 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   LEU D 373 " --> pdb=" O   MET D 369 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 368 through 373'
    Processing helix  chain 'D' and resid 394 through 403
      removed outlier: 3.592A  pdb=" N   SER D 402 " --> pdb=" O   ASP D 398 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ARG D 403 " --> pdb=" O   ARG D 399 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 405 through 412
      removed outlier: 4.348A  pdb=" N   GLN D 412 " --> pdb=" O   ALA D 408 " (cutoff:3.500A)

    560 hydrogen bonds defined for protein.
    1608 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: 1.85

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2444
        1.33 -     1.44: 2976
        1.44 -     1.56: 7856
        1.56 -     1.68: 12
        1.68 -     1.80: 52
  Bond restraints: 13340
  Sorted by residual:
  bond pdb=" O12 PGW B 501 "
       pdb=" P   PGW B 501 "
    ideal  model  delta    sigma   weight residual
    1.636  1.693 -0.057 2.00e-02 2.50e+03 8.04e+00
  bond pdb=" O12 PGW C 501 "
       pdb=" P   PGW C 501 "
    ideal  model  delta    sigma   weight residual
    1.636  1.693 -0.057 2.00e-02 2.50e+03 8.04e+00
  bond pdb=" O12 PGW D 501 "
       pdb=" P   PGW D 501 "
    ideal  model  delta    sigma   weight residual
    1.636  1.693 -0.057 2.00e-02 2.50e+03 8.04e+00
  bond pdb=" O12 PGW A 501 "
       pdb=" P   PGW A 501 "
    ideal  model  delta    sigma   weight residual
    1.636  1.693 -0.057 2.00e-02 2.50e+03 8.04e+00
  bond pdb=" C03 PGW D 501 "
       pdb=" O11 PGW D 501 "
    ideal  model  delta    sigma   weight residual
    1.412  1.363  0.049 2.00e-02 2.50e+03 6.11e+00
  ... (remaining 13335 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 16152
        2.05 -     4.10: 1288
        4.10 -     6.16: 340
        6.16 -     8.21: 184
        8.21 -    10.26: 48
  Bond angle restraints: 18012
  Sorted by residual:
  angle pdb=" C   ASP D  92 "
        pdb=" N   LEU D  93 "
        pdb=" CA  LEU D  93 "
      ideal   model   delta    sigma   weight residual
     121.54  131.80  -10.26 1.91e+00 2.74e-01 2.88e+01
  angle pdb=" C   ASP A  92 "
        pdb=" N   LEU A  93 "
        pdb=" CA  LEU A  93 "
      ideal   model   delta    sigma   weight residual
     121.54  131.80  -10.26 1.91e+00 2.74e-01 2.88e+01
  angle pdb=" C   ASP C  92 "
        pdb=" N   LEU C  93 "
        pdb=" CA  LEU C  93 "
      ideal   model   delta    sigma   weight residual
     121.54  131.80  -10.26 1.91e+00 2.74e-01 2.88e+01
  angle pdb=" C   ASP B  92 "
        pdb=" N   LEU B  93 "
        pdb=" CA  LEU B  93 "
      ideal   model   delta    sigma   weight residual
     121.54  131.80  -10.26 1.91e+00 2.74e-01 2.88e+01
  angle pdb=" N   LEU B  24 "
        pdb=" CA  LEU B  24 "
        pdb=" C   LEU B  24 "
      ideal   model   delta    sigma   weight residual
     111.36  105.70    5.66 1.09e+00 8.42e-01 2.69e+01
  ... (remaining 18007 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.86: 7904
       34.86 -    69.71: 164
       69.71 -   104.57: 20
      104.57 -   139.43: 8
      139.43 -   174.29: 4
  Dihedral angle restraints: 8100
    sinusoidal: 3512
      harmonic: 4588
  Sorted by residual:
  dihedral pdb=" C3' CMP A 500 "
           pdb=" O3' CMP A 500 "
           pdb=" P   CMP A 500 "
           pdb=" O1P CMP A 500 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  114.29 -174.29     1      2.00e+01 2.50e-03 4.79e+01
  dihedral pdb=" C3' CMP B 500 "
           pdb=" O3' CMP B 500 "
           pdb=" P   CMP B 500 "
           pdb=" O1P CMP B 500 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  114.29 -174.29     1      2.00e+01 2.50e-03 4.79e+01
  dihedral pdb=" C3' CMP D 500 "
           pdb=" O3' CMP D 500 "
           pdb=" P   CMP D 500 "
           pdb=" O1P CMP D 500 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  114.29 -174.29     1      2.00e+01 2.50e-03 4.79e+01
  ... (remaining 8097 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 1744
       0.092 -    0.185: 320
       0.185 -    0.277: 24
       0.277 -    0.369: 4
       0.369 -    0.461: 4
  Chirality restraints: 2096
  Sorted by residual:
  chirality pdb=" CB  ILE D  58 "
            pdb=" CA  ILE D  58 "
            pdb=" CG1 ILE D  58 "
            pdb=" CG2 ILE D  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.18    0.46 2.00e-01 2.50e+01 5.32e+00
  chirality pdb=" CB  ILE C  58 "
            pdb=" CA  ILE C  58 "
            pdb=" CG1 ILE C  58 "
            pdb=" CG2 ILE C  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.18    0.46 2.00e-01 2.50e+01 5.32e+00
  chirality pdb=" CB  ILE B  58 "
            pdb=" CA  ILE B  58 "
            pdb=" CG1 ILE B  58 "
            pdb=" CG2 ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.18    0.46 2.00e-01 2.50e+01 5.32e+00
  ... (remaining 2093 not shown)

  Planarity restraints: 2164
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C  93 "    0.018 2.00e-02 2.50e+03   3.68e-02 1.35e+01
        pdb=" C   LEU C  93 "   -0.064 2.00e-02 2.50e+03
        pdb=" O   LEU C  93 "    0.024 2.00e-02 2.50e+03
        pdb=" N   LEU C  94 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B  93 "    0.018 2.00e-02 2.50e+03   3.68e-02 1.35e+01
        pdb=" C   LEU B  93 "   -0.064 2.00e-02 2.50e+03
        pdb=" O   LEU B  93 "    0.024 2.00e-02 2.50e+03
        pdb=" N   LEU B  94 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D  93 "   -0.018 2.00e-02 2.50e+03   3.68e-02 1.35e+01
        pdb=" C   LEU D  93 "    0.064 2.00e-02 2.50e+03
        pdb=" O   LEU D  93 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   LEU D  94 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 2161 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 3328
        2.80 -     3.33: 11372
        3.33 -     3.85: 20892
        3.85 -     4.38: 23112
        4.38 -     4.90: 41884
  Nonbonded interactions: 100588
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 175 "
            pdb=" OD2 ASP B 188 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OH  TYR C 175 "
            pdb=" OD2 ASP C 188 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OH  TYR A 175 "
            pdb=" OD2 ASP A 188 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OH  TYR D 175 "
            pdb=" OD2 ASP D 188 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OH  TYR A 186 "
            pdb=" OG1 THR B 180 "
     model   vdw
     2.322 3.040
  ... (remaining 100583 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.480
  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:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     12.500
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
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      :  0.011   0.079  13340  Z= 0.455
  Angle     :  1.513  10.258  18012  Z= 0.706
  Chirality :  0.071   0.461   2096
  Planarity :  0.009   0.058   2164
  Dihedral  : 15.435 174.285   5140
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  6.87 %
    Favored  : 91.64 %
  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: -4.12 (0.17), residues: 1544
  helix: -2.63 (0.13), residues: 888
  sheet: -1.79 (0.46), residues: 92
  loop : -2.79 (0.24), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 124 
 TYR   0.026   0.004   TYR A 211 
 PHE   0.014   0.003   PHE A 365 
 TRP   0.019   0.003   TRP C 264 
 HIS   0.006   0.002   HIS B 292 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01074 /  0.46 (13340)
  covalent geometry    : angle       1.51333 /  0.71 (18012)
  hydrogen bonds       : bond        0.10497 /  6.77 (  560)
  hydrogen bonds       : angle       6.00402 /  4.07 ( 1608)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 232
  time to evaluate  : 0.424 
Fit side-chains
REVERT: B  171 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8558 (tp)
REVERT: B  233 ARG cc_start: 0.8393 (ttt90) cc_final: 0.8013 (mtp85)
REVERT: D  229 LYS cc_start: 0.9055 (tmtp) cc_final: 0.8847 (tttp)
  outliers start: 20
  outliers final: 3
  residues processed: 248
  average time/residue: 0.1541
  time to fit residues: 51.6117
Evaluate side-chains
  121 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 117
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain D residue  171 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0670
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    0.5980
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    0.8980
   chunk 149 optimal weight:    0.9990
   overall best weight:    0.6118

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.147704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.114875 restraints weight = 17296.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 2.63
r_work: 0.3007 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13340  Z= 0.133
  Angle     :  0.752   8.115  18012  Z= 0.343
  Chirality :  0.044   0.226   2096
  Planarity :  0.006   0.042   2164
  Dihedral  : 16.825 174.079   2200
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 13.06 %
    Favored  : 83.58 %
  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: -2.04 (0.21), residues: 1544
  helix: -0.63 (0.17), residues: 884
  sheet: -1.43 (0.49), residues: 92
  loop : -2.41 (0.25), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 399 
 TYR   0.015   0.001   TYR B 128 
 PHE   0.009   0.001   PHE A 302 
 TRP   0.014   0.002   TRP D 264 
 HIS   0.002   0.001   HIS D 149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 (13340)
  covalent geometry    : angle       0.75151 /  0.34 (18012)
  hydrogen bonds       : bond        0.03928 /  2.48 (  560)
  hydrogen bonds       : angle       4.14910 /  2.86 ( 1608)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 144
  time to evaluate  : 0.493 
Fit side-chains
REVERT: A  126 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.6887 (pp)
REVERT: A  171 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8499 (tp)
REVERT: A  233 ARG cc_start: 0.8459 (ttt90) cc_final: 0.8102 (mtp85)
REVERT: A  318 GLU cc_start: 0.8390 (tt0) cc_final: 0.8079 (mt-10)
REVERT: B  126 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6734 (pp)
REVERT: B  171 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8495 (tp)
REVERT: B  233 ARG cc_start: 0.8539 (ttt90) cc_final: 0.8220 (mtp85)
REVERT: B  318 GLU cc_start: 0.8368 (tt0) cc_final: 0.8076 (mt-10)
REVERT: C  126 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6821 (pp)
REVERT: C  171 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8494 (tp)
REVERT: C  233 ARG cc_start: 0.8383 (ttt90) cc_final: 0.8094 (mtp85)
REVERT: C  318 GLU cc_start: 0.8302 (tt0) cc_final: 0.7985 (mt-10)
REVERT: D  126 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6801 (pp)
REVERT: D  171 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8508 (tp)
REVERT: D  233 ARG cc_start: 0.8393 (ttt90) cc_final: 0.8093 (mtp85)
REVERT: D  318 GLU cc_start: 0.8360 (tt0) cc_final: 0.8056 (mt-10)
  outliers start: 45
  outliers final: 14
  residues processed: 187
  average time/residue: 0.1215
  time to fit residues: 33.3599
Evaluate side-chains
  151 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   80 SER
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  203 ILE
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain D residue   28 ILE
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  205 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 130 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   chunk 145 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 144 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 114 optimal weight:    6.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 119 GLN
** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 119 GLN
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 119 GLN
** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 119 GLN
** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.142695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.109212 restraints weight = 17725.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.81
r_work: 0.2873 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  13340  Z= 0.236
  Angle     :  0.789   8.993  18012  Z= 0.361
  Chirality :  0.049   0.257   2096
  Planarity :  0.005   0.043   2164
  Dihedral  : 16.155 171.270   2200
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 14.48 %
    Favored  : 80.52 %
  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: -1.45 (0.22), residues: 1544
  helix: -0.29 (0.18), residues: 924
  sheet: -1.12 (0.51), residues: 84
  loop : -1.99 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 384 
 TYR   0.014   0.002   TYR A 175 
 PHE   0.010   0.002   PHE C 309 
 TRP   0.010   0.002   TRP A 264 
 HIS   0.002   0.001   HIS B 281 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00583 /  0.24 (13340)
  covalent geometry    : angle       0.78906 /  0.36 (18012)
  hydrogen bonds       : bond        0.04345 /  2.76 (  560)
  hydrogen bonds       : angle       4.07120 /  2.79 ( 1608)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 126
  time to evaluate  : 0.512 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7386 (tt)
REVERT: A  126 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.6912 (pp)
REVERT: A  230 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8494 (tp)
REVERT: A  233 ARG cc_start: 0.8521 (ttt90) cc_final: 0.8180 (mtp85)
REVERT: A  272 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7836 (tp30)
REVERT: A  318 GLU cc_start: 0.8427 (tt0) cc_final: 0.8066 (mt-10)
REVERT: B   60 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7370 (tt)
REVERT: B  126 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7010 (pp)
REVERT: B  230 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8489 (tp)
REVERT: B  233 ARG cc_start: 0.8510 (ttt90) cc_final: 0.8175 (mtp85)
REVERT: B  272 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7803 (tp30)
REVERT: B  318 GLU cc_start: 0.8414 (tt0) cc_final: 0.8064 (mt-10)
REVERT: C   60 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7408 (tt)
REVERT: C  126 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.6945 (pp)
REVERT: C  230 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8470 (tp)
REVERT: C  233 ARG cc_start: 0.8416 (ttt90) cc_final: 0.8141 (mtp85)
REVERT: C  272 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7834 (tp30)
REVERT: C  318 GLU cc_start: 0.8416 (tt0) cc_final: 0.8076 (mt-10)
REVERT: D   60 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7386 (tt)
REVERT: D  126 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.6943 (pp)
REVERT: D  230 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8502 (tp)
REVERT: D  233 ARG cc_start: 0.8427 (ttt90) cc_final: 0.8147 (mtp85)
REVERT: D  272 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7827 (tp30)
REVERT: D  318 GLU cc_start: 0.8415 (tt0) cc_final: 0.8060 (mt-10)
  outliers start: 67
  outliers final: 25
  residues processed: 188
  average time/residue: 0.1235
  time to fit residues: 33.9223
Evaluate side-chains
  160 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 119
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  224 LYS
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  224 LYS
Chi-restraints excluded: chain B residue  229 LYS
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  359 ILE
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  203 ILE
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  224 LYS
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  359 ILE
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  224 LYS
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  272 GLU
Chi-restraints excluded: chain D residue  359 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 73 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   chunk 144 optimal weight:    4.9990
   chunk 27 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 92 optimal weight:    0.6980
   chunk 77 optimal weight:    7.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    1.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.146572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.113947 restraints weight = 17473.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 2.56
r_work: 0.2890 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2739 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  13340  Z= 0.131
  Angle     :  0.688   9.006  18012  Z= 0.308
  Chirality :  0.044   0.253   2096
  Planarity :  0.005   0.042   2164
  Dihedral  : 15.265 170.978   2200
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 14.93 %
    Favored  : 80.97 %
  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: -0.96 (0.22), residues: 1544
  helix:  0.09 (0.18), residues: 932
  sheet: -1.05 (0.50), residues: 84
  loop : -1.79 (0.28), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 399 
 TYR   0.008   0.001   TYR A 175 
 PHE   0.008   0.001   PHE D 365 
 TRP   0.012   0.001   TRP D 264 
 HIS   0.001   0.001   HIS C 149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.13 (13340)
  covalent geometry    : angle       0.68841 /  0.31 (18012)
  hydrogen bonds       : bond        0.03645 /  2.29 (  560)
  hydrogen bonds       : angle       3.75387 /  2.57 ( 1608)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 141
  time to evaluate  : 0.553 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7357 (tt)
REVERT: A  114 LYS cc_start: 0.8194 (tptp) cc_final: 0.7856 (tttp)
REVERT: A  126 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.6914 (pp)
REVERT: A  205 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8888 (mm)
REVERT: A  230 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8598 (tp)
REVERT: A  233 ARG cc_start: 0.8647 (ttt90) cc_final: 0.8278 (mtp85)
REVERT: A  272 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7795 (tp30)
REVERT: A  318 GLU cc_start: 0.8651 (tt0) cc_final: 0.8300 (mt-10)
REVERT: A  389 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8819 (pp)
REVERT: B   60 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7370 (tt)
REVERT: B  114 LYS cc_start: 0.8192 (tptp) cc_final: 0.7848 (tttp)
REVERT: B  126 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.6933 (pp)
REVERT: B  205 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8889 (mm)
REVERT: B  230 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8595 (tp)
REVERT: B  233 ARG cc_start: 0.8640 (ttt90) cc_final: 0.8272 (mtp85)
REVERT: B  272 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7748 (tp30)
REVERT: B  318 GLU cc_start: 0.8630 (tt0) cc_final: 0.8290 (mt-10)
REVERT: C   60 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7379 (tt)
REVERT: C  114 LYS cc_start: 0.8225 (tptp) cc_final: 0.7841 (tttp)
REVERT: C  126 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.6910 (pp)
REVERT: C  205 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8895 (mm)
REVERT: C  230 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8587 (tp)
REVERT: C  233 ARG cc_start: 0.8566 (ttt90) cc_final: 0.8249 (mtp85)
REVERT: C  272 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7766 (tp30)
REVERT: C  318 GLU cc_start: 0.8622 (tt0) cc_final: 0.8277 (mt-10)
REVERT: D   60 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7335 (tt)
REVERT: D  114 LYS cc_start: 0.8223 (tptp) cc_final: 0.7831 (tttp)
REVERT: D  126 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6863 (pp)
REVERT: D  205 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8887 (mm)
REVERT: D  230 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8591 (tp)
REVERT: D  233 ARG cc_start: 0.8574 (ttt90) cc_final: 0.8252 (mtp85)
REVERT: D  272 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7772 (tp30)
REVERT: D  318 GLU cc_start: 0.8634 (tt0) cc_final: 0.8275 (mt-10)
  outliers start: 55
  outliers final: 20
  residues processed: 193
  average time/residue: 0.1318
  time to fit residues: 36.2139
Evaluate side-chains
  169 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 128
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  203 ILE
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  276 LEU
Chi-restraints excluded: chain C residue  314 ILE
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  272 GLU
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  314 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 130 optimal weight:    0.9990
   chunk 117 optimal weight:    8.9990
   chunk 98 optimal weight:    0.9990
   chunk 145 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 131 optimal weight:    0.9990
   chunk 2 optimal weight:    0.3980
   chunk 90 optimal weight:    0.6980
   chunk 140 optimal weight:    0.6980
   chunk 148 optimal weight:    4.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 253 GLN
** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.146840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.113401 restraints weight = 17584.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 2.68
r_work: 0.3039 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  13340  Z= 0.116
  Angle     :  0.660   8.841  18012  Z= 0.294
  Chirality :  0.043   0.282   2096
  Planarity :  0.004   0.042   2164
  Dihedral  : 14.361 168.508   2200
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 15.00 %
    Favored  : 80.22 %
  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: -0.41 (0.22), residues: 1544
  helix:  0.54 (0.18), residues: 908
  sheet: -0.75 (0.49), residues: 92
  loop : -1.48 (0.28), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 124 
 TYR   0.008   0.001   TYR A 175 
 PHE   0.007   0.001   PHE B 365 
 TRP   0.009   0.001   TRP C 264 
 HIS   0.002   0.001   HIS D 149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.12 (13340)
  covalent geometry    : angle       0.65981 /  0.29 (18012)
  hydrogen bonds       : bond        0.03398 /  2.13 (  560)
  hydrogen bonds       : angle       3.55073 /  2.42 ( 1608)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 136
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7224 (tt)
REVERT: A  114 LYS cc_start: 0.8129 (tptp) cc_final: 0.7755 (tttp)
REVERT: A  126 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6877 (pp)
REVERT: A  230 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8535 (tp)
REVERT: A  233 ARG cc_start: 0.8429 (ttt90) cc_final: 0.8056 (mtp85)
REVERT: A  272 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7655 (tp30)
REVERT: A  318 GLU cc_start: 0.8419 (tt0) cc_final: 0.8060 (mt-10)
REVERT: A  389 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8607 (pp)
REVERT: B   60 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7231 (tt)
REVERT: B  114 LYS cc_start: 0.8147 (tptp) cc_final: 0.7768 (tttp)
REVERT: B  126 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6897 (pp)
REVERT: B  230 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8514 (tp)
REVERT: B  233 ARG cc_start: 0.8431 (ttt90) cc_final: 0.8047 (mtp85)
REVERT: B  272 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7629 (tp30)
REVERT: B  318 GLU cc_start: 0.8401 (tt0) cc_final: 0.8039 (mt-10)
REVERT: C   60 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7226 (tt)
REVERT: C  114 LYS cc_start: 0.8171 (tptp) cc_final: 0.7782 (tttp)
REVERT: C  126 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.6897 (pp)
REVERT: C  230 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8507 (tp)
REVERT: C  233 ARG cc_start: 0.8358 (ttt90) cc_final: 0.8033 (mtp85)
REVERT: C  272 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7638 (tp30)
REVERT: C  318 GLU cc_start: 0.8397 (tt0) cc_final: 0.8032 (mt-10)
REVERT: D   60 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7232 (tt)
REVERT: D  114 LYS cc_start: 0.8194 (tptp) cc_final: 0.7767 (tttp)
REVERT: D  126 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6932 (pp)
REVERT: D  230 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8514 (tp)
REVERT: D  233 ARG cc_start: 0.8371 (ttt90) cc_final: 0.8046 (mtp85)
REVERT: D  272 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7635 (tp30)
REVERT: D  318 GLU cc_start: 0.8406 (tt0) cc_final: 0.8041 (mt-10)
  outliers start: 64
  outliers final: 22
  residues processed: 197
  average time/residue: 0.1272
  time to fit residues: 36.1610
Evaluate side-chains
  164 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 125
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  203 ILE
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  276 LEU
Chi-restraints excluded: chain C residue  314 ILE
Chi-restraints excluded: chain C residue  359 ILE
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  272 GLU
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  314 ILE
Chi-restraints excluded: chain D residue  359 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 17 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 113 optimal weight:    0.5980
   chunk 107 optimal weight:    5.9990
   chunk 12 optimal weight:    0.5980
   chunk 77 optimal weight:    7.9990
   chunk 124 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 138 optimal weight:    0.3980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 253 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.148771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.116298 restraints weight = 17366.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 2.46
r_work: 0.2949 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2798 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  13340  Z= 0.113
  Angle     :  0.661   8.837  18012  Z= 0.291
  Chirality :  0.043   0.270   2096
  Planarity :  0.004   0.041   2164
  Dihedral  : 13.956 167.912   2200
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 15.67 %
    Favored  : 80.90 %
  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: -0.04 (0.22), residues: 1544
  helix:  0.78 (0.18), residues: 908
  sheet: -0.52 (0.50), residues: 92
  loop : -1.26 (0.28), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 124 
 TYR   0.008   0.001   TYR C 175 
 PHE   0.006   0.001   PHE D 242 
 TRP   0.009   0.001   TRP A 264 
 HIS   0.002   0.001   HIS C 149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.11 (13340)
  covalent geometry    : angle       0.66076 /  0.29 (18012)
  hydrogen bonds       : bond        0.03347 /  2.11 (  560)
  hydrogen bonds       : angle       3.37939 /  2.30 ( 1608)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 128
  time to evaluate  : 0.510 
Fit side-chains
REVERT: A   47 ASP cc_start: 0.7150 (m-30) cc_final: 0.6945 (m-30)
REVERT: A   60 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7303 (tt)
REVERT: A  126 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6778 (pp)
REVERT: A  230 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8559 (tp)
REVERT: A  233 ARG cc_start: 0.8530 (ttt90) cc_final: 0.8156 (mtp85)
REVERT: A  272 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.7879 (tp30)
REVERT: A  318 GLU cc_start: 0.8633 (tt0) cc_final: 0.8237 (mt-10)
REVERT: A  389 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8718 (pp)
REVERT: B   47 ASP cc_start: 0.7157 (m-30) cc_final: 0.6952 (m-30)
REVERT: B   60 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7300 (tt)
REVERT: B  114 LYS cc_start: 0.8144 (tptp) cc_final: 0.7763 (tttp)
REVERT: B  126 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6834 (pp)
REVERT: B  230 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8551 (tp)
REVERT: B  233 ARG cc_start: 0.8526 (ttt90) cc_final: 0.8150 (mtp85)
REVERT: B  272 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7748 (tp30)
REVERT: B  318 GLU cc_start: 0.8603 (tt0) cc_final: 0.8182 (mt-10)
REVERT: C   47 ASP cc_start: 0.7157 (m-30) cc_final: 0.6942 (m-30)
REVERT: C   60 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7316 (tt)
REVERT: C  114 LYS cc_start: 0.8250 (tptp) cc_final: 0.7849 (tttp)
REVERT: C  126 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6834 (pp)
REVERT: C  230 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8542 (tp)
REVERT: C  233 ARG cc_start: 0.8477 (ttt90) cc_final: 0.8146 (mtp85)
REVERT: C  272 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.7750 (tp30)
REVERT: C  318 GLU cc_start: 0.8605 (tt0) cc_final: 0.8191 (mt-10)
REVERT: D   47 ASP cc_start: 0.7131 (m-30) cc_final: 0.6922 (m-30)
REVERT: D  114 LYS cc_start: 0.8261 (tptp) cc_final: 0.7851 (tttp)
REVERT: D  126 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6809 (pp)
REVERT: D  230 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8542 (tp)
REVERT: D  233 ARG cc_start: 0.8483 (ttt90) cc_final: 0.8146 (mtp85)
REVERT: D  272 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.7740 (tp30)
REVERT: D  318 GLU cc_start: 0.8607 (tt0) cc_final: 0.8185 (mt-10)
  outliers start: 46
  outliers final: 26
  residues processed: 172
  average time/residue: 0.1239
  time to fit residues: 31.1786
Evaluate side-chains
  164 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 122
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain B residue  359 ILE
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  203 ILE
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  276 LEU
Chi-restraints excluded: chain C residue  314 ILE
Chi-restraints excluded: chain C residue  359 ILE
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  272 GLU
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  314 ILE
Chi-restraints excluded: chain D residue  359 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 70 optimal weight:    5.9990
   chunk 51 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 115 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 146 optimal weight:    4.9990
   chunk 71 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.146573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.113639 restraints weight = 17386.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 2.70
r_work: 0.2870 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.2961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  13340  Z= 0.145
  Angle     :  0.667   8.529  18012  Z= 0.298
  Chirality :  0.044   0.263   2096
  Planarity :  0.004   0.042   2164
  Dihedral  : 14.002 167.980   2200
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 16.49 %
    Favored  : 79.78 %
  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:  0.03 (0.22), residues: 1544
  helix:  0.77 (0.18), residues: 916
  sheet: -0.36 (0.49), residues: 84
  loop : -1.14 (0.28), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 111 
 TYR   0.010   0.001   TYR D 175 
 PHE   0.006   0.001   PHE D 309 
 TRP   0.008   0.001   TRP C 264 
 HIS   0.002   0.001   HIS C 281 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.15 (13340)
  covalent geometry    : angle       0.66748 /  0.30 (18012)
  hydrogen bonds       : bond        0.03656 /  2.30 (  560)
  hydrogen bonds       : angle       3.44475 /  2.34 ( 1608)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 113
  time to evaluate  : 0.509 
Fit side-chains
REVERT: A  126 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6828 (pp)
REVERT: A  230 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8531 (tp)
REVERT: A  233 ARG cc_start: 0.8410 (ttt90) cc_final: 0.8012 (mtp85)
REVERT: A  272 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7772 (tp30)
REVERT: A  318 GLU cc_start: 0.8457 (tt0) cc_final: 0.8041 (mt-10)
REVERT: A  389 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8631 (pp)
REVERT: B   47 ASP cc_start: 0.7019 (m-30) cc_final: 0.6773 (m-30)
REVERT: B  114 LYS cc_start: 0.8159 (tptp) cc_final: 0.7740 (tttp)
REVERT: B  126 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6835 (pp)
REVERT: B  230 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8528 (tp)
REVERT: B  233 ARG cc_start: 0.8404 (ttt90) cc_final: 0.8006 (mtp85)
REVERT: B  272 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7772 (tp30)
REVERT: B  318 GLU cc_start: 0.8457 (tt0) cc_final: 0.8039 (mt-10)
REVERT: C   47 ASP cc_start: 0.7107 (m-30) cc_final: 0.6859 (m-30)
REVERT: C  114 LYS cc_start: 0.8155 (tptp) cc_final: 0.7738 (tttp)
REVERT: C  126 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6826 (pp)
REVERT: C  230 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8535 (tp)
REVERT: C  233 ARG cc_start: 0.8365 (ttt90) cc_final: 0.8009 (mtp85)
REVERT: C  272 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7656 (tp30)
REVERT: C  318 GLU cc_start: 0.8479 (tt0) cc_final: 0.8055 (mt-10)
REVERT: D   47 ASP cc_start: 0.7167 (m-30) cc_final: 0.6923 (m-30)
REVERT: D  114 LYS cc_start: 0.8250 (tptp) cc_final: 0.7810 (tttp)
REVERT: D  126 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6828 (pp)
REVERT: D  230 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8541 (tp)
REVERT: D  233 ARG cc_start: 0.8369 (ttt90) cc_final: 0.8008 (mtp85)
REVERT: D  272 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7648 (tp30)
REVERT: D  318 GLU cc_start: 0.8456 (tt0) cc_final: 0.8038 (mt-10)
  outliers start: 50
  outliers final: 24
  residues processed: 161
  average time/residue: 0.1201
  time to fit residues: 28.6651
Evaluate side-chains
  150 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 113
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain B residue  359 ILE
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  203 ILE
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  276 LEU
Chi-restraints excluded: chain C residue  314 ILE
Chi-restraints excluded: chain C residue  359 ILE
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  272 GLU
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  314 ILE
Chi-restraints excluded: chain D residue  359 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 105 optimal weight:    0.0020
   chunk 119 optimal weight:    0.1980
   chunk 53 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 30 optimal weight:    0.3980
   chunk 107 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 152 optimal weight:    7.9990
   chunk 115 optimal weight:    0.5980
   overall best weight:    0.4388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.149957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.117390 restraints weight = 17304.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 2.55
r_work: 0.2973 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  13340  Z= 0.100
  Angle     :  0.627   8.915  18012  Z= 0.277
  Chirality :  0.042   0.256   2096
  Planarity :  0.004   0.040   2164
  Dihedral  : 13.507 166.590   2200
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 16.42 %
    Favored  : 80.45 %
  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:  0.44 (0.23), residues: 1544
  helix:  1.09 (0.18), residues: 908
  sheet: -0.34 (0.51), residues: 92
  loop : -0.89 (0.29), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 399 
 TYR   0.007   0.001   TYR A 175 
 PHE   0.006   0.001   PHE D  40 
 TRP   0.010   0.001   TRP A 264 
 HIS   0.002   0.001   HIS B 149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00218 /  0.10 (13340)
  covalent geometry    : angle       0.62653 /  0.28 (18012)
  hydrogen bonds       : bond        0.03144 /  1.97 (  560)
  hydrogen bonds       : angle       3.26747 /  2.23 ( 1608)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 146
  time to evaluate  : 0.508 
Fit side-chains
REVERT: A  126 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6817 (pp)
REVERT: A  230 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8549 (tp)
REVERT: A  233 ARG cc_start: 0.8307 (ttt90) cc_final: 0.7909 (mtp85)
REVERT: A  272 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7703 (tp30)
REVERT: A  318 GLU cc_start: 0.8365 (tt0) cc_final: 0.8011 (mt-10)
REVERT: A  334 MET cc_start: 0.7376 (ttt) cc_final: 0.6891 (tpp)
REVERT: A  389 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8566 (pp)
REVERT: B   47 ASP cc_start: 0.7073 (m-30) cc_final: 0.6750 (m-30)
REVERT: B  114 LYS cc_start: 0.8192 (tptp) cc_final: 0.7795 (tttp)
REVERT: B  126 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6770 (pp)
REVERT: B  230 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8540 (tp)
REVERT: B  233 ARG cc_start: 0.8297 (ttt90) cc_final: 0.7900 (mtp85)
REVERT: B  272 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7682 (tp30)
REVERT: B  318 GLU cc_start: 0.8344 (tt0) cc_final: 0.7994 (mt-10)
REVERT: B  334 MET cc_start: 0.7392 (ttt) cc_final: 0.6921 (tpp)
REVERT: C   47 ASP cc_start: 0.7063 (m-30) cc_final: 0.6741 (m-30)
REVERT: C  114 LYS cc_start: 0.8191 (tptp) cc_final: 0.7779 (tttp)
REVERT: C  126 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6774 (pp)
REVERT: C  230 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8546 (tp)
REVERT: C  233 ARG cc_start: 0.8306 (ttt90) cc_final: 0.7962 (mtp85)
REVERT: C  272 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7683 (tp30)
REVERT: C  318 GLU cc_start: 0.8338 (tt0) cc_final: 0.7983 (mt-10)
REVERT: C  334 MET cc_start: 0.7377 (ttt) cc_final: 0.6895 (tpp)
REVERT: D   47 ASP cc_start: 0.7045 (m-30) cc_final: 0.6729 (m-30)
REVERT: D  114 LYS cc_start: 0.8205 (tptp) cc_final: 0.7783 (tttp)
REVERT: D  126 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6793 (pp)
REVERT: D  230 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8547 (tp)
REVERT: D  233 ARG cc_start: 0.8306 (ttt90) cc_final: 0.7958 (mtp85)
REVERT: D  272 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7697 (tp30)
REVERT: D  318 GLU cc_start: 0.8340 (tt0) cc_final: 0.7983 (mt-10)
REVERT: D  334 MET cc_start: 0.7377 (ttt) cc_final: 0.6894 (tpp)
  outliers start: 42
  outliers final: 16
  residues processed: 186
  average time/residue: 0.1176
  time to fit residues: 32.2886
Evaluate side-chains
  154 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 125
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  203 ILE
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  276 LEU
Chi-restraints excluded: chain C residue  401 LEU
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  272 GLU
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  401 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 135 optimal weight:    1.9990
   chunk 153 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 144 optimal weight:    0.7980
   chunk 115 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0980
   chunk 103 optimal weight:    0.6980
   chunk 94 optimal weight:    0.7980
   chunk 154 optimal weight:    4.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 253 GLN
** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.147832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.114272 restraints weight = 17431.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.75
r_work: 0.3006 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  13340  Z= 0.111
  Angle     :  0.630   7.560  18012  Z= 0.281
  Chirality :  0.042   0.258   2096
  Planarity :  0.004   0.037   2164
  Dihedral  : 13.423 166.558   2200
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 17.61 %
    Favored  : 80.00 %
  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:  0.62 (0.23), residues: 1544
  helix:  1.17 (0.18), residues: 908
  sheet: -0.26 (0.51), residues: 92
  loop : -0.68 (0.30), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 124 
 TYR   0.007   0.001   TYR A 175 
 PHE   0.006   0.001   PHE C  40 
 TRP   0.008   0.001   TRP D 264 
 HIS   0.002   0.001   HIS A 149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.11 (13340)
  covalent geometry    : angle       0.63034 /  0.28 (18012)
  hydrogen bonds       : bond        0.03245 /  2.04 (  560)
  hydrogen bonds       : angle       3.17342 /  2.17 ( 1608)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 122
  time to evaluate  : 0.487 
Fit side-chains
REVERT: A  126 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6822 (pp)
REVERT: A  230 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8575 (tp)
REVERT: A  233 ARG cc_start: 0.8386 (ttt90) cc_final: 0.7978 (mtp85)
REVERT: A  272 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7795 (tp30)
REVERT: A  318 GLU cc_start: 0.8458 (tt0) cc_final: 0.8093 (mt-10)
REVERT: A  334 MET cc_start: 0.7627 (ttt) cc_final: 0.7150 (tpp)
REVERT: A  389 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8662 (pp)
REVERT: B  114 LYS cc_start: 0.8247 (tptp) cc_final: 0.7830 (tttp)
REVERT: B  126 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6852 (pp)
REVERT: B  230 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8566 (tp)
REVERT: B  233 ARG cc_start: 0.8380 (ttt90) cc_final: 0.7969 (mtp85)
REVERT: B  272 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7770 (tp30)
REVERT: B  318 GLU cc_start: 0.8449 (tt0) cc_final: 0.8080 (mt-10)
REVERT: B  334 MET cc_start: 0.7630 (ttt) cc_final: 0.7164 (tpp)
REVERT: C  126 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6845 (pp)
REVERT: C  230 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8577 (tp)
REVERT: C  233 ARG cc_start: 0.8352 (ttt90) cc_final: 0.7986 (mtp85)
REVERT: C  272 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7669 (tp30)
REVERT: C  318 GLU cc_start: 0.8421 (tt0) cc_final: 0.8069 (mt-10)
REVERT: C  334 MET cc_start: 0.7631 (ttt) cc_final: 0.7163 (tpp)
REVERT: D  126 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6804 (pp)
REVERT: D  230 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8576 (tp)
REVERT: D  233 ARG cc_start: 0.8352 (ttt90) cc_final: 0.7982 (mtp85)
REVERT: D  265 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8186 (tm-30)
REVERT: D  272 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7764 (tp30)
REVERT: D  318 GLU cc_start: 0.8451 (tt0) cc_final: 0.8091 (mt-10)
REVERT: D  334 MET cc_start: 0.7637 (ttt) cc_final: 0.7169 (tpp)
  outliers start: 32
  outliers final: 10
  residues processed: 154
  average time/residue: 0.1251
  time to fit residues: 28.1269
Evaluate side-chains
  142 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain C residue  203 ILE
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  276 LEU
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  272 GLU
Chi-restraints excluded: chain D residue  276 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 99 optimal weight:    0.7980
   chunk 125 optimal weight:    4.9990
   chunk 41 optimal weight:    0.2980
   chunk 55 optimal weight:    0.0370
   chunk 17 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0270
   overall best weight:    0.3716

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.139527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.103310 restraints weight = 18117.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 3.23
r_work: 0.2907 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.3467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  13340  Z= 0.099
  Angle     :  0.620   7.825  18012  Z= 0.273
  Chirality :  0.042   0.258   2096
  Planarity :  0.004   0.037   2164
  Dihedral  : 13.008 165.718   2192
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 17.99 %
    Favored  : 80.22 %
  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:  0.89 (0.23), residues: 1544
  helix:  1.34 (0.18), residues: 912
  sheet: -0.23 (0.51), residues: 92
  loop : -0.48 (0.31), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 124 
 TYR   0.006   0.001   TYR B 175 
 PHE   0.007   0.001   PHE A  40 
 TRP   0.011   0.001   TRP B 264 
 HIS   0.002   0.000   HIS A 149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00210 /  0.10 (13340)
  covalent geometry    : angle       0.61964 /  0.27 (18012)
  hydrogen bonds       : bond        0.03030 /  1.91 (  560)
  hydrogen bonds       : angle       3.07100 /  2.10 ( 1608)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 0.513 
Fit side-chains
REVERT: A  126 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6778 (pp)
REVERT: A  233 ARG cc_start: 0.8313 (ttt90) cc_final: 0.7929 (mtp85)
REVERT: A  272 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.7795 (tp30)
REVERT: A  318 GLU cc_start: 0.8471 (tt0) cc_final: 0.8053 (mt-10)
REVERT: A  334 MET cc_start: 0.7491 (ttt) cc_final: 0.6981 (tpp)
REVERT: B  114 LYS cc_start: 0.8197 (tptp) cc_final: 0.7815 (tttp)
REVERT: B  126 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6739 (pp)
REVERT: B  233 ARG cc_start: 0.8314 (ttt90) cc_final: 0.7917 (mtp85)
REVERT: B  272 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.7786 (tp30)
REVERT: B  318 GLU cc_start: 0.8463 (tt0) cc_final: 0.8035 (mt-10)
REVERT: B  334 MET cc_start: 0.7506 (ttt) cc_final: 0.7009 (tpp)
REVERT: C  126 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6777 (pp)
REVERT: C  233 ARG cc_start: 0.8281 (ttt90) cc_final: 0.7931 (mtp85)
REVERT: C  272 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.7784 (tp30)
REVERT: C  318 GLU cc_start: 0.8454 (tt0) cc_final: 0.8040 (mt-10)
REVERT: C  334 MET cc_start: 0.7522 (ttt) cc_final: 0.7020 (tpp)
REVERT: D  126 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6744 (pp)
REVERT: D  233 ARG cc_start: 0.8278 (ttt90) cc_final: 0.7929 (mtp85)
REVERT: D  265 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8257 (tm-30)
REVERT: D  272 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7787 (tp30)
REVERT: D  318 GLU cc_start: 0.8472 (tt0) cc_final: 0.8047 (mt-10)
REVERT: D  334 MET cc_start: 0.7501 (ttt) cc_final: 0.6998 (tpp)
REVERT: D  395 GLU cc_start: 0.8159 (pt0) cc_final: 0.7856 (pt0)
  outliers start: 24
  outliers final: 5
  residues processed: 152
  average time/residue: 0.1299
  time to fit residues: 28.3345
Evaluate side-chains
  131 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  276 LEU
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  272 GLU
Chi-restraints excluded: chain D residue  276 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 119 optimal weight:    0.2980
   chunk 146 optimal weight:    0.6980
   chunk 13 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 144 optimal weight:    0.0040
   chunk 149 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    0.1980
   chunk 30 optimal weight:    0.9980
   chunk 108 optimal weight:    0.6980
   chunk 151 optimal weight:    2.9990
   overall best weight:    0.3592

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 253 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.147588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.113549 restraints weight = 17405.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 2.77
r_work: 0.2924 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.3584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  13340  Z= 0.099
  Angle     :  0.642  13.418  18012  Z= 0.278
  Chirality :  0.042   0.260   2096
  Planarity :  0.004   0.036   2164
  Dihedral  : 12.908 165.713   2192
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 18.96 %
    Favored  : 79.70 %
  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:  1.11 (0.23), residues: 1544
  helix:  1.50 (0.18), residues: 912
  sheet: -0.18 (0.51), residues: 92
  loop : -0.34 (0.31), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 124 
 TYR   0.005   0.001   TYR A 259 
 PHE   0.006   0.001   PHE A  40 
 TRP   0.008   0.001   TRP C 264 
 HIS   0.002   0.000   HIS C 149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00214 /  0.10 (13340)
  covalent geometry    : angle       0.64246 /  0.28 (18012)
  hydrogen bonds       : bond        0.03001 /  1.91 (  560)
  hydrogen bonds       : angle       2.95880 /  2.03 ( 1608)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2827.97 seconds
wall clock time: 49 minutes 27.69 seconds (2967.69 seconds total)