Starting phenix.real_space_refine
on Sat Aug 23 16:33:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6cju_7484/08_2025/6cju_7484.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6cju_7484/08_2025/6cju_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6cju_7484/08_2025/6cju_7484.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6cju_7484/08_2025/6cju_7484.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6cju_7484/08_2025/6cju_7484.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6cju_7484/08_2025/6cju_7484.map"
  }
  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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: {'RNA': 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: 265
          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: 2.61, per 1000 atoms: 0.20
  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: 1.11
  Conformation dependent library (CDL) restraints added in 768.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.39
  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: 1.63

  Time building geometry restraints manager: 1.56 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: 16168
        2.05 -     4.10: 1280
        4.10 -     6.16: 332
        6.16 -     8.21: 184
        8.21 -    10.26: 48
  Bond angle restraints: 18012
  Sorted by residual:
  angle pdb=" C4' CMP A 500 "
        pdb=" C3' CMP A 500 "
        pdb=" O3' CMP A 500 "
      ideal   model   delta    sigma   weight residual
     113.00  104.61    8.39 1.50e+00 4.44e-01 3.13e+01
  angle pdb=" C4' CMP B 500 "
        pdb=" C3' CMP B 500 "
        pdb=" O3' CMP B 500 "
      ideal   model   delta    sigma   weight residual
     113.00  104.61    8.39 1.50e+00 4.44e-01 3.13e+01
  angle pdb=" C4' CMP D 500 "
        pdb=" C3' CMP D 500 "
        pdb=" O3' CMP D 500 "
      ideal   model   delta    sigma   weight residual
     113.00  104.61    8.39 1.50e+00 4.44e-01 3.13e+01
  angle pdb=" C4' CMP C 500 "
        pdb=" C3' CMP C 500 "
        pdb=" O3' CMP C 500 "
      ideal   model   delta    sigma   weight residual
     113.00  104.61    8.39 1.50e+00 4.44e-01 3.13e+01
  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
  ... (remaining 18007 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.88: 7924
       34.88 -    69.76: 180
       69.76 -   104.64: 24
      104.64 -   139.52: 24
      139.52 -   174.39: 16
  Dihedral angle restraints: 8168
    sinusoidal: 3580
      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 8165 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 1740
       0.092 -    0.185: 324
       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: 0.03
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:             1.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     11.400
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
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= 0.457
  Angle     :  1.507  10.258  18012  Z= 0.715
  Chirality :  0.071   0.461   2096
  Planarity :  0.009   0.058   2164
  Dihedral  : 18.925 174.394   5208
  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 aren 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
  covalent geometry    : bond        0.01075 (13340)
  covalent geometry    : angle       1.50713 (18012)
  hydrogen bonds       : bond        0.10497 (  560)
  hydrogen bonds       : angle       6.00402 ( 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  : 0.467 
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: 0.9054 (tmtp) cc_final: 0.8847 (tttp)
  outliers start: 20
  outliers final: 3
  residues processed: 248
  average time/residue: 0.1441
  time to fit residues: 47.8335
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  : 0.296 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3746 r_free = 0.3746 target = 0.147896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.115047 restraints weight = 17275.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 2.65
r_work: 0.3028 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.1771

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= 0.128
  Angle     :  0.724   7.298  18012  Z= 0.341
  Chirality :  0.043   0.223   2096
  Planarity :  0.006   0.041   2164
  Dihedral  : 21.831 166.593   2268
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.04
  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 aren not related in a simple way.
  whole: -2.02 (0.21), residues: 1544
  helix: -0.62 (0.17), residues: 884
  sheet: -1.40 (0.49), residues: 92
  loop : -2.39 (0.25), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 399 
 TYR   0.014   0.001   TYR B 128 
 PHE   0.009   0.001   PHE D 302 
 TRP   0.014   0.002   TRP D 264 
 HIS   0.002   0.001   HIS D 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (13340)
  covalent geometry    : angle       0.72440 (18012)
  hydrogen bonds       : bond        0.03903 (  560)
  hydrogen bonds       : angle       4.13948 ( 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
  190 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 145
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A  126 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6833 (pp)
REVERT: A  171 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8445 (tp)
REVERT: A  233 ARG cc_start: 0.8417 (ttt90) cc_final: 0.8135 (mtp85)
REVERT: A  318 GLU cc_start: 0.8390 (tt0) cc_final: 0.8018 (mt-10)
REVERT: B  126 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6713 (pp)
REVERT: B  171 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8442 (tp)
REVERT: B  233 ARG cc_start: 0.8429 (ttt90) cc_final: 0.8163 (mtp85)
REVERT: B  318 GLU cc_start: 0.8330 (tt0) cc_final: 0.7943 (mt-10)
REVERT: C  126 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6751 (pp)
REVERT: C  171 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8438 (tp)
REVERT: C  233 ARG cc_start: 0.8261 (ttt90) cc_final: 0.8035 (mtp85)
REVERT: C  303 LYS cc_start: 0.7226 (tppt) cc_final: 0.7025 (mmtm)
REVERT: C  318 GLU cc_start: 0.8297 (tt0) cc_final: 0.7942 (mt-10)
REVERT: D  126 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6736 (pp)
REVERT: D  171 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8455 (tp)
REVERT: D  233 ARG cc_start: 0.8282 (ttt90) cc_final: 0.8040 (mtp85)
REVERT: D  318 GLU cc_start: 0.8320 (tt0) cc_final: 0.7956 (mt-10)
  outliers start: 45
  outliers final: 11
  residues processed: 190
  average time/residue: 0.1054
  time to fit residues: 29.1766
Evaluate side-chains
  145 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
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  205 LEU
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 B residue  248 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  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:    3.9990
   chunk 145 optimal weight:    0.0980
   chunk 70 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0670
   chunk 144 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 114 optimal weight:    0.7980
   overall best weight:    0.9920

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

Flipped N/Q/H residues before XYZ refinement:
A 119 GLN
** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 119 GLN
B 253 GLN
C 119 GLN
C 253 GLN
D 119 GLN
** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.142743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.108007 restraints weight = 17717.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 2.79
r_work: 0.2847 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13340  Z= 0.136
  Angle     :  0.689   9.311  18012  Z= 0.318
  Chirality :  0.044   0.252   2096
  Planarity :  0.005   0.043   2164
  Dihedral  : 19.657 166.595   2268
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  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 aren not related in a simple way.
  whole: -1.14 (0.22), residues: 1544
  helix: -0.10 (0.18), residues: 932
  sheet: -0.99 (0.52), residues: 92
  loop : -1.78 (0.28), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 399 
 TYR   0.011   0.001   TYR A 128 
 PHE   0.008   0.001   PHE C 309 
 TRP   0.010   0.001   TRP A 264 
 HIS   0.002   0.001   HIS D 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (13340)
  covalent geometry    : angle       0.68884 (18012)
  hydrogen bonds       : bond        0.03601 (  560)
  hydrogen bonds       : angle       3.77702 ( 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
  191 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 136
  time to evaluate  : 0.444 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7265 (tt)
REVERT: A  126 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6735 (pp)
REVERT: A  205 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8725 (mm)
REVERT: A  230 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8546 (tp)
REVERT: A  233 ARG cc_start: 0.8484 (ttt90) cc_final: 0.8143 (mtp85)
REVERT: A  272 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7828 (tp30)
REVERT: A  318 GLU cc_start: 0.8384 (tt0) cc_final: 0.8046 (mt-10)
REVERT: B   60 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7270 (tt)
REVERT: B  126 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6868 (pp)
REVERT: B  205 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8742 (mm)
REVERT: B  230 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8526 (tp)
REVERT: B  233 ARG cc_start: 0.8482 (ttt90) cc_final: 0.8148 (mtp85)
REVERT: B  272 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7632 (tp30)
REVERT: B  318 GLU cc_start: 0.8405 (tt0) cc_final: 0.8048 (mt-10)
REVERT: C   60 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7277 (tt)
REVERT: C  126 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.6778 (pp)
REVERT: C  205 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8741 (mm)
REVERT: C  230 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8520 (tp)
REVERT: C  233 ARG cc_start: 0.8388 (ttt90) cc_final: 0.8114 (mtp85)
REVERT: C  272 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7639 (tp30)
REVERT: C  318 GLU cc_start: 0.8390 (tt0) cc_final: 0.8006 (mt-10)
REVERT: D   60 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7343 (tt)
REVERT: D  126 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6791 (pp)
REVERT: D  205 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8722 (mm)
REVERT: D  230 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8516 (tp)
REVERT: D  233 ARG cc_start: 0.8397 (ttt90) cc_final: 0.8116 (mtp85)
REVERT: D  272 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7621 (tp30)
REVERT: D  318 GLU cc_start: 0.8412 (tt0) cc_final: 0.8016 (mt-10)
  outliers start: 55
  outliers final: 6
  residues processed: 185
  average time/residue: 0.1145
  time to fit residues: 30.2640
Evaluate side-chains
  143 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
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  203 ILE
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  126 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  230 LEU
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue  126 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  272 GLU
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue  126 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  272 GLU
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:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 144 optimal weight:    0.0470
   chunk 27 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 124 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   chunk 77 optimal weight:    0.0970
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.4676

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.3765 r_free = 0.3765 target = 0.149728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.117093 restraints weight = 17378.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 2.60
r_work: 0.2954 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2664

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= 0.105
  Angle     :  0.633   9.166  18012  Z= 0.291
  Chirality :  0.042   0.253   2096
  Planarity :  0.004   0.041   2164
  Dihedral  : 18.170 165.677   2260
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 15.07 %
    Favored  : 81.42 %
  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 aren not related in a simple way.
  whole: -0.46 (0.22), residues: 1544
  helix:  0.52 (0.18), residues: 908
  sheet: -0.85 (0.51), residues: 92
  loop : -1.56 (0.28), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 399 
 TYR   0.008   0.001   TYR A 128 
 PHE   0.006   0.001   PHE D 309 
 TRP   0.012   0.001   TRP D 264 
 HIS   0.002   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (13340)
  covalent geometry    : angle       0.63292 (18012)
  hydrogen bonds       : bond        0.03250 (  560)
  hydrogen bonds       : angle       3.55022 ( 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: 47
    poor density    : 149
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7313 (tt)
REVERT: A  114 LYS cc_start: 0.8075 (tptp) cc_final: 0.7754 (tttp)
REVERT: A  126 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6786 (pp)
REVERT: A  230 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8529 (tp)
REVERT: A  233 ARG cc_start: 0.8437 (ttt90) cc_final: 0.8082 (mtp85)
REVERT: A  272 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7645 (tp30)
REVERT: A  318 GLU cc_start: 0.8353 (tt0) cc_final: 0.8009 (mt-10)
REVERT: A  389 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8559 (pp)
REVERT: B   60 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7260 (tt)
REVERT: B  126 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6762 (pp)
REVERT: B  233 ARG cc_start: 0.8411 (ttt90) cc_final: 0.8059 (mtp85)
REVERT: B  272 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7785 (tp30)
REVERT: B  318 GLU cc_start: 0.8335 (tt0) cc_final: 0.8019 (mt-10)
REVERT: B  389 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8570 (pp)
REVERT: C   60 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7319 (tt)
REVERT: C  114 LYS cc_start: 0.8227 (tptp) cc_final: 0.7889 (tttp)
REVERT: C  126 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6723 (pp)
REVERT: C  230 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8533 (tp)
REVERT: C  233 ARG cc_start: 0.8305 (ttt90) cc_final: 0.8029 (mtp85)
REVERT: C  272 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7780 (tp30)
REVERT: C  318 GLU cc_start: 0.8340 (tt0) cc_final: 0.8006 (mt-10)
REVERT: C  389 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8557 (pp)
REVERT: D   60 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7334 (tt)
REVERT: D  114 LYS cc_start: 0.8214 (tptp) cc_final: 0.7870 (tttp)
REVERT: D  126 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6753 (pp)
REVERT: D  229 LYS cc_start: 0.9020 (tttt) cc_final: 0.8735 (tptm)
REVERT: D  233 ARG cc_start: 0.8344 (ttt90) cc_final: 0.8031 (mtp85)
REVERT: D  272 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7644 (tp30)
REVERT: D  318 GLU cc_start: 0.8345 (tt0) cc_final: 0.8009 (mt-10)
REVERT: D  389 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8621 (pp)
  outliers start: 47
  outliers final: 15
  residues processed: 196
  average time/residue: 0.1050
  time to fit residues: 29.7078
Evaluate side-chains
  161 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 128
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
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  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  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  203 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 B residue  389 LEU
Chi-restraints excluded: chain C residue   60 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 C residue  314 ILE
Chi-restraints excluded: chain C residue  359 ILE
Chi-restraints excluded: chain C residue  389 LEU
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  203 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
Chi-restraints excluded: chain D residue  389 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 130 optimal weight:    0.8980
   chunk 117 optimal weight:    8.9990
   chunk 98 optimal weight:    1.9990
   chunk 145 optimal weight:    1.9990
   chunk 37 optimal weight:    6.9990
   chunk 131 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0470
   chunk 90 optimal weight:    0.9990
   chunk 140 optimal weight:    0.8980
   chunk 148 optimal weight:    1.9990
   overall best weight:    0.7278

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.3750 r_free = 0.3750 target = 0.148272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.115372 restraints weight = 17521.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 2.60
r_work: 0.2909 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2900

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= 0.118
  Angle     :  0.661  13.596  18012  Z= 0.298
  Chirality :  0.043   0.272   2096
  Planarity :  0.004   0.040   2164
  Dihedral  : 17.517 165.525   2260
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 15.67 %
    Favored  : 80.67 %
  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 aren not related in a simple way.
  whole: -0.50 (0.23), residues: 1544
  helix:  0.44 (0.18), residues: 952
  sheet: -0.55 (0.51), residues: 92
  loop : -1.69 (0.29), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 399 
 TYR   0.008   0.001   TYR D 175 
 PHE   0.008   0.001   PHE B 365 
 TRP   0.010   0.001   TRP D 264 
 HIS   0.002   0.001   HIS D 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (13340)
  covalent geometry    : angle       0.66140 (18012)
  hydrogen bonds       : bond        0.03322 (  560)
  hydrogen bonds       : angle       3.34592 ( 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
  168 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 119
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7195 (tt)
REVERT: A  230 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8511 (tp)
REVERT: A  233 ARG cc_start: 0.8423 (ttt90) cc_final: 0.8054 (mtp85)
REVERT: A  272 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7599 (tp30)
REVERT: A  318 GLU cc_start: 0.8409 (tt0) cc_final: 0.8009 (mt-10)
REVERT: A  389 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8532 (pp)
REVERT: B   60 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7153 (tt)
REVERT: B  114 LYS cc_start: 0.8205 (tptp) cc_final: 0.7901 (tttp)
REVERT: B  229 LYS cc_start: 0.9018 (tttp) cc_final: 0.8743 (tttt)
REVERT: B  233 ARG cc_start: 0.8431 (ttt90) cc_final: 0.8042 (mtp85)
REVERT: B  272 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7820 (tp30)
REVERT: B  318 GLU cc_start: 0.8402 (tt0) cc_final: 0.8020 (mt-10)
REVERT: B  389 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8546 (pp)
REVERT: C   60 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7210 (tt)
REVERT: C  114 LYS cc_start: 0.8204 (tptp) cc_final: 0.7861 (tttp)
REVERT: C  230 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8479 (tp)
REVERT: C  233 ARG cc_start: 0.8322 (ttt90) cc_final: 0.8029 (mtp85)
REVERT: C  272 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7623 (tp30)
REVERT: C  318 GLU cc_start: 0.8397 (tt0) cc_final: 0.8018 (mt-10)
REVERT: C  389 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8570 (pp)
REVERT: D   60 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7198 (tt)
REVERT: D  114 LYS cc_start: 0.8242 (tptp) cc_final: 0.7843 (tttp)
REVERT: D  126 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6825 (pp)
REVERT: D  233 ARG cc_start: 0.8343 (ttt90) cc_final: 0.8020 (mtp85)
REVERT: D  272 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7778 (tp30)
REVERT: D  318 GLU cc_start: 0.8403 (tt0) cc_final: 0.8019 (mt-10)
REVERT: D  389 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8560 (pp)
  outliers start: 49
  outliers final: 17
  residues processed: 168
  average time/residue: 0.1128
  time to fit residues: 27.1210
Evaluate side-chains
  151 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 119
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue   60 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  314 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain B residue   40 PHE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  359 ILE
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain C residue   40 PHE
Chi-restraints excluded: chain C residue   60 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  359 ILE
Chi-restraints excluded: chain C residue  389 LEU
Chi-restraints excluded: chain D residue   40 PHE
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  203 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
Chi-restraints excluded: chain D residue  389 LEU
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:    0.7980
   chunk 45 optimal weight:    0.0670
   chunk 62 optimal weight:    0.9980
   chunk 113 optimal weight:    0.9980
   chunk 107 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 77 optimal weight:    8.9990
   chunk 124 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0370
   chunk 138 optimal weight:    3.9990
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
A 253 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.150911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.117080 restraints weight = 17323.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.32
r_work: 0.3117 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.3113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  13340  Z= 0.106
  Angle     :  0.645  11.189  18012  Z= 0.288
  Chirality :  0.042   0.253   2096
  Planarity :  0.004   0.039   2164
  Dihedral  : 16.607 165.195   2260
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 16.49 %
    Favored  : 80.60 %
  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 aren not related in a simple way.
  whole: -0.10 (0.23), residues: 1544
  helix:  0.68 (0.18), residues: 948
  sheet: -0.43 (0.51), residues: 92
  loop : -1.33 (0.30), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 124 
 TYR   0.007   0.001   TYR B 175 
 PHE   0.007   0.001   PHE D 365 
 TRP   0.010   0.001   TRP B 264 
 HIS   0.001   0.001   HIS D 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 (13340)
  covalent geometry    : angle       0.64457 (18012)
  hydrogen bonds       : bond        0.03132 (  560)
  hydrogen bonds       : angle       3.22417 ( 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
  161 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 122
  time to evaluate  : 0.492 
Fit side-chains
REVERT: A   47 ASP cc_start: 0.7247 (m-30) cc_final: 0.7010 (m-30)
REVERT: A  233 ARG cc_start: 0.8540 (ttt90) cc_final: 0.8162 (mtp85)
REVERT: A  272 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.7930 (tp30)
REVERT: A  318 GLU cc_start: 0.8604 (tt0) cc_final: 0.8210 (mt-10)
REVERT: A  389 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8699 (pp)
REVERT: B   47 ASP cc_start: 0.7259 (m-30) cc_final: 0.7056 (m-30)
REVERT: B  114 LYS cc_start: 0.8276 (tptp) cc_final: 0.7915 (tttp)
REVERT: B  229 LYS cc_start: 0.9021 (tttp) cc_final: 0.8736 (tttt)
REVERT: B  233 ARG cc_start: 0.8559 (ttt90) cc_final: 0.8152 (mtp85)
REVERT: B  272 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.7924 (tp30)
REVERT: B  318 GLU cc_start: 0.8592 (tt0) cc_final: 0.8208 (mt-10)
REVERT: B  389 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8691 (pp)
REVERT: C   47 ASP cc_start: 0.7265 (m-30) cc_final: 0.7034 (m-30)
REVERT: C  114 LYS cc_start: 0.8259 (tptp) cc_final: 0.7884 (tttp)
REVERT: C  233 ARG cc_start: 0.8461 (ttt90) cc_final: 0.8145 (mtp85)
REVERT: C  272 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7894 (tp30)
REVERT: C  303 LYS cc_start: 0.7032 (mmtm) cc_final: 0.6303 (mptt)
REVERT: C  318 GLU cc_start: 0.8587 (tt0) cc_final: 0.8211 (mt-10)
REVERT: C  389 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8710 (pp)
REVERT: D   47 ASP cc_start: 0.7245 (m-30) cc_final: 0.7012 (m-30)
REVERT: D  114 LYS cc_start: 0.8285 (tptp) cc_final: 0.7895 (tttp)
REVERT: D  233 ARG cc_start: 0.8507 (ttt90) cc_final: 0.8161 (mtp85)
REVERT: D  272 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.7903 (tp30)
REVERT: D  318 GLU cc_start: 0.8609 (tt0) cc_final: 0.8233 (mt-10)
REVERT: D  389 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8716 (pp)
  outliers start: 39
  outliers final: 15
  residues processed: 161
  average time/residue: 0.1102
  time to fit residues: 25.5370
Evaluate side-chains
  141 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue  203 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   40 PHE
Chi-restraints excluded: chain B residue  203 ILE
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  389 LEU
Chi-restraints excluded: chain C residue   40 PHE
Chi-restraints excluded: chain C residue  203 ILE
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  276 LEU
Chi-restraints excluded: chain C residue  389 LEU
Chi-restraints excluded: chain D residue   40 PHE
Chi-restraints excluded: chain D residue  203 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  389 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 70 optimal weight:    6.9990
   chunk 51 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 104 optimal weight:    0.0070
   chunk 115 optimal weight:    0.9990
   chunk 6 optimal weight:    0.3980
   chunk 146 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 67 optimal weight:    0.0370
   overall best weight:    0.4476

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.151310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.117874 restraints weight = 17306.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.35
r_work: 0.2978 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2828 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.3265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  13340  Z= 0.103
  Angle     :  0.624   9.944  18012  Z= 0.281
  Chirality :  0.042   0.247   2096
  Planarity :  0.004   0.039   2164
  Dihedral  : 16.193 164.982   2260
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.94 %
    Favored  : 81.12 %
  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 aren not related in a simple way.
  whole:  0.15 (0.23), residues: 1544
  helix:  0.83 (0.18), residues: 948
  sheet: -0.32 (0.51), residues: 92
  loop : -1.13 (0.30), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 124 
 TYR   0.006   0.001   TYR A 175 
 PHE   0.005   0.001   PHE D 365 
 TRP   0.009   0.001   TRP A 264 
 HIS   0.001   0.000   HIS D 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 (13340)
  covalent geometry    : angle       0.62403 (18012)
  hydrogen bonds       : bond        0.03040 (  560)
  hydrogen bonds       : angle       3.12038 ( 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
  147 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.494 
Fit side-chains
REVERT: A   39 LEU cc_start: 0.8021 (mp) cc_final: 0.7821 (mt)
REVERT: A   47 ASP cc_start: 0.7299 (m-30) cc_final: 0.7040 (m-30)
REVERT: A  233 ARG cc_start: 0.8497 (ttt90) cc_final: 0.8080 (mtp85)
REVERT: A  272 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7915 (tp30)
REVERT: A  318 GLU cc_start: 0.8608 (tt0) cc_final: 0.8200 (mt-10)
REVERT: A  389 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8686 (pp)
REVERT: B   39 LEU cc_start: 0.8031 (mp) cc_final: 0.7822 (mt)
REVERT: B   47 ASP cc_start: 0.7310 (m-30) cc_final: 0.7045 (m-30)
REVERT: B  114 LYS cc_start: 0.8300 (tptp) cc_final: 0.7940 (tttp)
REVERT: B  233 ARG cc_start: 0.8544 (ttt90) cc_final: 0.8121 (mtp85)
REVERT: B  272 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7885 (tp30)
REVERT: B  318 GLU cc_start: 0.8599 (tt0) cc_final: 0.8192 (mt-10)
REVERT: B  389 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8684 (pp)
REVERT: C   39 LEU cc_start: 0.8068 (mp) cc_final: 0.7849 (mt)
REVERT: C   47 ASP cc_start: 0.7290 (m-30) cc_final: 0.7034 (m-30)
REVERT: C  114 LYS cc_start: 0.8290 (tptp) cc_final: 0.7911 (tttp)
REVERT: C  233 ARG cc_start: 0.8433 (ttt90) cc_final: 0.8067 (mtp85)
REVERT: C  272 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.7913 (tp30)
REVERT: C  318 GLU cc_start: 0.8609 (tt0) cc_final: 0.8209 (mt-10)
REVERT: C  389 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8695 (pp)
REVERT: D   39 LEU cc_start: 0.8056 (mp) cc_final: 0.7840 (mt)
REVERT: D   47 ASP cc_start: 0.7285 (m-30) cc_final: 0.7031 (m-30)
REVERT: D  114 LYS cc_start: 0.8298 (tptp) cc_final: 0.7908 (tttp)
REVERT: D  233 ARG cc_start: 0.8484 (ttt90) cc_final: 0.8122 (mtp85)
REVERT: D  272 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.7891 (tp30)
REVERT: D  318 GLU cc_start: 0.8616 (tt0) cc_final: 0.8220 (mt-10)
REVERT: D  389 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8685 (pp)
  outliers start: 26
  outliers final: 14
  residues processed: 145
  average time/residue: 0.1195
  time to fit residues: 24.7014
Evaluate side-chains
  138 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 116
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue  203 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   40 PHE
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain C residue   40 PHE
Chi-restraints excluded: chain C residue  203 ILE
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  276 LEU
Chi-restraints excluded: chain C residue  359 ILE
Chi-restraints excluded: chain C residue  389 LEU
Chi-restraints excluded: chain D residue   40 PHE
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  272 GLU
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  389 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0000
   chunk 119 optimal weight:    0.3980
   chunk 53 optimal weight:    3.9990
   chunk 84 optimal weight:    0.0470
   chunk 64 optimal weight:    0.0040
   chunk 30 optimal weight:    0.8980
   chunk 107 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 152 optimal weight:    7.9990
   chunk 115 optimal weight:    1.9990
   overall best weight:    0.2694

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.153128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.119711 restraints weight = 17257.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 2.38
r_work: 0.3158 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3007 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.3469

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= 0.098
  Angle     :  0.607   9.375  18012  Z= 0.273
  Chirality :  0.041   0.250   2096
  Planarity :  0.004   0.036   2164
  Dihedral  : 15.966 164.709   2260
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 17.69 %
    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 aren not related in a simple way.
  whole:  0.47 (0.23), residues: 1544
  helix:  1.03 (0.18), residues: 952
  sheet: -0.21 (0.52), residues: 92
  loop : -0.88 (0.32), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 124 
 TYR   0.005   0.001   TYR D 175 
 PHE   0.005   0.001   PHE A 309 
 TRP   0.010   0.001   TRP B 264 
 HIS   0.002   0.001   HIS C 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 (13340)
  covalent geometry    : angle       0.60708 (18012)
  hydrogen bonds       : bond        0.02867 (  560)
  hydrogen bonds       : angle       3.00384 ( 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
  162 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.514 
Fit side-chains
REVERT: A   47 ASP cc_start: 0.7278 (m-30) cc_final: 0.7006 (m-30)
REVERT: A  233 ARG cc_start: 0.8465 (ttt90) cc_final: 0.8063 (mtp85)
REVERT: A  272 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.7941 (tp30)
REVERT: A  318 GLU cc_start: 0.8567 (tt0) cc_final: 0.8164 (mt-10)
REVERT: A  389 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8688 (pp)
REVERT: B   47 ASP cc_start: 0.7311 (m-30) cc_final: 0.7088 (m-30)
REVERT: B  114 LYS cc_start: 0.8286 (tptp) cc_final: 0.7936 (tttp)
REVERT: B  233 ARG cc_start: 0.8504 (ttt90) cc_final: 0.8094 (mtp85)
REVERT: B  272 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.7910 (tp30)
REVERT: B  318 GLU cc_start: 0.8573 (tt0) cc_final: 0.8166 (mt-10)
REVERT: B  389 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8683 (pp)
REVERT: C   47 ASP cc_start: 0.7265 (m-30) cc_final: 0.7009 (m-30)
REVERT: C  114 LYS cc_start: 0.8273 (tptp) cc_final: 0.7900 (tttp)
REVERT: C  233 ARG cc_start: 0.8388 (ttt90) cc_final: 0.8023 (mtp85)
REVERT: C  272 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.7932 (tp30)
REVERT: C  318 GLU cc_start: 0.8561 (tt0) cc_final: 0.8166 (mt-10)
REVERT: C  389 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8688 (pp)
REVERT: D   47 ASP cc_start: 0.7271 (m-30) cc_final: 0.7006 (m-30)
REVERT: D  114 LYS cc_start: 0.8317 (tptp) cc_final: 0.7925 (tttp)
REVERT: D  229 LYS cc_start: 0.8991 (tttt) cc_final: 0.8652 (tttp)
REVERT: D  233 ARG cc_start: 0.8447 (ttt90) cc_final: 0.8068 (mtp85)
REVERT: D  265 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8234 (tm-30)
REVERT: D  272 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.7921 (tp30)
REVERT: D  318 GLU cc_start: 0.8562 (tt0) cc_final: 0.8179 (mt-10)
REVERT: D  389 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8705 (pp)
  outliers start: 19
  outliers final: 10
  residues processed: 156
  average time/residue: 0.1160
  time to fit residues: 25.9390
Evaluate side-chains
  146 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 PHE
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  395 GLU
Chi-restraints excluded: chain B residue   40 PHE
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain C residue   40 PHE
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  276 LEU
Chi-restraints excluded: chain C residue  389 LEU
Chi-restraints excluded: chain D residue   40 PHE
Chi-restraints excluded: chain D residue  272 GLU
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  389 LEU
Chi-restraints excluded: chain D residue  395 GLU
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:    0.6980
   chunk 153 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 144 optimal weight:    0.0060
   chunk 115 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 103 optimal weight:    3.9990
   chunk 94 optimal weight:    0.0270
   chunk 154 optimal weight:    2.9990
   overall best weight:    0.4654

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.152432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.120080 restraints weight = 17317.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 2.36
r_work: 0.3047 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.3558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  13340  Z= 0.103
  Angle     :  0.646  17.276  18012  Z= 0.283
  Chirality :  0.041   0.248   2096
  Planarity :  0.004   0.034   2164
  Dihedral  : 15.880 164.655   2260
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 18.51 %
    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 aren not related in a simple way.
  whole:  0.58 (0.23), residues: 1544
  helix:  1.12 (0.18), residues: 956
  sheet: -0.17 (0.52), residues: 92
  loop : -0.86 (0.32), residues: 496

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   0.005   0.001   PHE D 365 
 TRP   0.009   0.001   TRP A 264 
 HIS   0.002   0.000   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 (13340)
  covalent geometry    : angle       0.64584 (18012)
  hydrogen bonds       : bond        0.02891 (  560)
  hydrogen bonds       : angle       2.92317 ( 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
  142 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 0.447 
Fit side-chains
REVERT: A   47 ASP cc_start: 0.7261 (m-30) cc_final: 0.7009 (m-30)
REVERT: A  233 ARG cc_start: 0.8568 (ttt90) cc_final: 0.8130 (mtp85)
REVERT: A  272 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.7918 (tp30)
REVERT: A  318 GLU cc_start: 0.8602 (tt0) cc_final: 0.8223 (mt-10)
REVERT: B   47 ASP cc_start: 0.7277 (m-30) cc_final: 0.7025 (m-30)
REVERT: B  114 LYS cc_start: 0.8387 (tptp) cc_final: 0.8021 (tttp)
REVERT: B  233 ARG cc_start: 0.8608 (ttt90) cc_final: 0.8179 (mtp85)
REVERT: B  272 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.7922 (tp30)
REVERT: B  318 GLU cc_start: 0.8592 (tt0) cc_final: 0.8221 (mt-10)
REVERT: C   47 ASP cc_start: 0.7260 (m-30) cc_final: 0.7013 (m-30)
REVERT: C  114 LYS cc_start: 0.8390 (tptp) cc_final: 0.7988 (tttp)
REVERT: C  233 ARG cc_start: 0.8503 (ttt90) cc_final: 0.8106 (mtp85)
REVERT: C  272 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.7943 (tp30)
REVERT: C  318 GLU cc_start: 0.8598 (tt0) cc_final: 0.8225 (mt-10)
REVERT: D   47 ASP cc_start: 0.7253 (m-30) cc_final: 0.7008 (m-30)
REVERT: D  114 LYS cc_start: 0.8432 (tptp) cc_final: 0.8013 (tttp)
REVERT: D  229 LYS cc_start: 0.8985 (tttt) cc_final: 0.8627 (tttp)
REVERT: D  233 ARG cc_start: 0.8545 (ttt90) cc_final: 0.8140 (mtp85)
REVERT: D  265 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8339 (tm-30)
REVERT: D  272 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.7925 (tp30)
REVERT: D  318 GLU cc_start: 0.8603 (tt0) cc_final: 0.8227 (mt-10)
  outliers start: 20
  outliers final: 10
  residues processed: 135
  average time/residue: 0.1115
  time to fit residues: 21.6645
Evaluate side-chains
  130 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  395 GLU
Chi-restraints excluded: chain B residue   40 PHE
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain C residue   40 PHE
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  276 LEU
Chi-restraints excluded: chain D residue   40 PHE
Chi-restraints excluded: chain D residue  272 GLU
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  395 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 22 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 86 optimal weight:    0.3980
   chunk 99 optimal weight:    0.9990
   chunk 125 optimal weight:    0.0000
   chunk 41 optimal weight:    0.5980
   chunk 55 optimal weight:    0.5980
   chunk 17 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.4384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.152727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.120643 restraints weight = 17495.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 2.44
r_work: 0.3146 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.3623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  13340  Z= 0.101
  Angle     :  0.637  16.670  18012  Z= 0.279
  Chirality :  0.041   0.250   2096
  Planarity :  0.004   0.034   2164
  Dihedral  : 15.763 164.626   2260
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 19.18 %
    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 aren not related in a simple way.
  whole:  0.75 (0.24), residues: 1544
  helix:  1.25 (0.18), residues: 956
  sheet: -0.25 (0.51), residues: 92
  loop : -0.75 (0.33), residues: 496

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   0.006   0.001   PHE C 340 
 TRP   0.010   0.001   TRP C 264 
 HIS   0.002   0.000   HIS D 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 (13340)
  covalent geometry    : angle       0.63687 (18012)
  hydrogen bonds       : bond        0.02882 (  560)
  hydrogen bonds       : angle       2.91014 ( 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
  134 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.481 
Fit side-chains
REVERT: A   47 ASP cc_start: 0.7230 (m-30) cc_final: 0.6972 (m-30)
REVERT: A  233 ARG cc_start: 0.8562 (ttt90) cc_final: 0.8123 (mtp85)
REVERT: A  272 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.7848 (tp30)
REVERT: A  318 GLU cc_start: 0.8593 (tt0) cc_final: 0.8218 (mt-10)
REVERT: B   47 ASP cc_start: 0.7261 (m-30) cc_final: 0.7004 (m-30)
REVERT: B  114 LYS cc_start: 0.8380 (tptp) cc_final: 0.8014 (tttp)
REVERT: B  233 ARG cc_start: 0.8613 (ttt90) cc_final: 0.8180 (mtp85)
REVERT: B  272 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.7951 (tp30)
REVERT: B  318 GLU cc_start: 0.8584 (tt0) cc_final: 0.8219 (mt-10)
REVERT: C   47 ASP cc_start: 0.7240 (m-30) cc_final: 0.6985 (m-30)
REVERT: C  114 LYS cc_start: 0.8390 (tptp) cc_final: 0.7984 (tttp)
REVERT: C  233 ARG cc_start: 0.8557 (ttt90) cc_final: 0.8157 (mtp85)
REVERT: C  272 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7865 (tp30)
REVERT: C  318 GLU cc_start: 0.8590 (tt0) cc_final: 0.8217 (mt-10)
REVERT: D   47 ASP cc_start: 0.7239 (m-30) cc_final: 0.6983 (m-30)
REVERT: D  114 LYS cc_start: 0.8428 (tptp) cc_final: 0.8006 (tttp)
REVERT: D  233 ARG cc_start: 0.8535 (ttt90) cc_final: 0.8135 (mtp85)
REVERT: D  272 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.7862 (tp30)
REVERT: D  318 GLU cc_start: 0.8604 (tt0) cc_final: 0.8228 (mt-10)
  outliers start: 15
  outliers final: 10
  residues processed: 128
  average time/residue: 0.1264
  time to fit residues: 22.8252
Evaluate side-chains
  133 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  395 GLU
Chi-restraints excluded: chain B residue   40 PHE
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain C residue   40 PHE
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  276 LEU
Chi-restraints excluded: chain D residue   40 PHE
Chi-restraints excluded: chain D residue  272 GLU
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  395 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 119 optimal weight:    0.0670
   chunk 146 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 58 optimal weight:    3.9990
   chunk 144 optimal weight:    0.0030
   chunk 149 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 108 optimal weight:    0.0040
   chunk 151 optimal weight:    0.8980
   overall best weight:    0.2740

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.142815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.107185 restraints weight = 17825.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 3.04
r_work: 0.2938 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.3771

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= 0.097
  Angle     :  0.629  16.825  18012  Z= 0.275
  Chirality :  0.041   0.252   2096
  Planarity :  0.004   0.034   2164
  Dihedral  : 15.590 164.218   2260
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 19.33 %
    Favored  : 79.55 %
  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 aren not related in a simple way.
  whole:  0.94 (0.24), residues: 1544
  helix:  1.43 (0.18), residues: 956
  sheet: -0.71 (0.45), residues: 116
  loop : -0.59 (0.34), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 124 
 TYR   0.005   0.001   TYR B 175 
 PHE   0.005   0.001   PHE C 242 
 TRP   0.010   0.001   TRP B 264 
 HIS   0.002   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 (13340)
  covalent geometry    : angle       0.62905 (18012)
  hydrogen bonds       : bond        0.02752 (  560)
  hydrogen bonds       : angle       2.85591 ( 1608)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2659.66 seconds
wall clock time: 46 minutes 15.68 seconds (2775.68 seconds total)