Starting phenix.real_space_refine
on Thu Mar 13 04:01:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kic_37257/03_2025/8kic_37257.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kic_37257/03_2025/8kic_37257.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kic_37257/03_2025/8kic_37257.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kic_37257/03_2025/8kic_37257.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kic_37257/03_2025/8kic_37257.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kic_37257/03_2025/8kic_37257.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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: 4
    Type Number    sf(0)   Gaussians
     S      17      5.16       5
     C    5374      2.51       5
     N    1515      2.21       5
     O    1683      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8589
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "D"
      Number of atoms: 632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 632
          Classifications: {'peptide': 87}
          Link IDs: {'PTRANS': 3, 'TRANS': 83}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 656
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 3, 'TRANS': 86}
    Chain: "F"
      Number of atoms: 667
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 667
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 3, 'TRANS': 87}
    Chain: "C"
      Number of atoms: 2178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 300, 2178
          Classifications: {'peptide': 300}
          Link IDs: {'PTRANS': 12, 'TRANS': 287}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 300, 2178
          Classifications: {'peptide': 300}
          Link IDs: {'PTRANS': 12, 'TRANS': 287}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 300, 2178
          Classifications: {'peptide': 300}
          Link IDs: {'PTRANS': 12, 'TRANS': 287}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 40
          Classifications: {'peptide': 8}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'TRANS': 7}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'UNK:plan-1': 8}
          Unresolved non-hydrogen planarities: 8
    Chain: "H"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 25
          Classifications: {'peptide': 5}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'TRANS': 4}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'UNK:plan-1': 5}
          Unresolved non-hydrogen planarities: 5
    Chain: "I"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 35
          Classifications: {'peptide': 7}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'UNK:plan-1': 7}
          Unresolved non-hydrogen planarities: 7
  Time building chain proxies: 5.84, per 1000 atoms: 0.68
  Number of scatterers: 8589
  At special positions: 0
  Unit cell: (89.04, 125.504, 122.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      17     16.00
     O    1683      8.00
     N    1515      7.00
     C    5374      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: 1.99
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2094

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 20 sheets defined
      21.8% alpha, 36.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.24
  Creating SS restraints...
    Processing helix  chain 'D' and resid 372 through 376
    Processing helix  chain 'D' and resid 401 through 407
    Processing helix  chain 'D' and resid 424 through 433
    Processing helix  chain 'E' and resid 372 through 376
    Processing helix  chain 'E' and resid 401 through 407
    Processing helix  chain 'E' and resid 424 through 433
    Processing helix  chain 'F' and resid 372 through 376
    Processing helix  chain 'F' and resid 401 through 407
    Processing helix  chain 'F' and resid 424 through 433
    Processing helix  chain 'C' and resid 42 through 50
      removed outlier: 4.200A  pdb=" N   LYS C  48 " --> pdb=" O   PRO C  44 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   VAL C  49 " --> pdb=" O   MET C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 158 through 162
      removed outlier: 3.513A  pdb=" N   LEU C 162 " --> pdb=" O   SER C 159 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 173 through 177
      removed outlier: 3.658A  pdb=" N   GLY C 176 " --> pdb=" O   ASN C 173 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 248 through 262
    Processing helix  chain 'C' and resid 277 through 285
    Processing helix  chain 'C' and resid 301 through 307
    Processing helix  chain 'C' and resid 324 through 335
      removed outlier: 3.808A  pdb=" N   LEU C 328 " --> pdb=" O   SER C 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 50
      removed outlier: 4.467A  pdb=" N   LYS A  48 " --> pdb=" O   PRO A  44 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   VAL A  49 " --> pdb=" O   MET A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 112
    Processing helix  chain 'A' and resid 158 through 162
      removed outlier: 3.607A  pdb=" N   LEU A 162 " --> pdb=" O   SER A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 177
      removed outlier: 3.592A  pdb=" N   GLY A 176 " --> pdb=" O   ASN A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 261
    Processing helix  chain 'A' and resid 277 through 282
    Processing helix  chain 'A' and resid 301 through 307
    Processing helix  chain 'A' and resid 324 through 335
      removed outlier: 3.611A  pdb=" N   LEU A 328 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 50
      removed outlier: 4.233A  pdb=" N   LYS B  48 " --> pdb=" O   PRO B  44 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   VAL B  49 " --> pdb=" O   MET B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 112
      removed outlier: 3.835A  pdb=" N   ILE B 111 " --> pdb=" O   ASN B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 162
      removed outlier: 3.541A  pdb=" N   LYS B 161 " --> pdb=" O   ASP B 158 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU B 162 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 158 through 162'
    Processing helix  chain 'B' and resid 173 through 177
      removed outlier: 3.731A  pdb=" N   GLY B 176 " --> pdb=" O   ASN B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 261
    Processing helix  chain 'B' and resid 279 through 284
    Processing helix  chain 'B' and resid 301 through 307
    Processing helix  chain 'B' and resid 324 through 335
      removed outlier: 3.741A  pdb=" N   LEU B 328 " --> pdb=" O   SER B 324 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 366 through 367
    Processing sheet with id=AA2, first strand: chain 'D' and resid 382 through 384
    Processing sheet with id=AA3, first strand: chain 'E' and resid 366 through 367
      removed outlier: 3.716A  pdb=" N   LEU E 380 " --> pdb=" O   ALA E 366 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLU E 396 " --> pdb=" O   THR E 379 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 382 through 384
    Processing sheet with id=AA5, first strand: chain 'E' and resid 439 through 440
      removed outlier: 3.865A  pdb=" N   ILE E 439 " --> pdb=" O   MET E 454 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 378 through 384
      removed outlier: 6.387A  pdb=" N   THR F 379 " --> pdb=" O   ASP F 395 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 60
      removed outlier: 7.938A  pdb=" N   SER C  93 " --> pdb=" O   ASN C 107 " (cutoff:3.500A)
      removed outlier: 4.928A  pdb=" N   ASN C 107 " --> pdb=" O   SER C  93 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   TYR C 103 " --> pdb=" O   ILE C  97 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ILE C 140 " --> pdb=" O   SER C 134 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   SER C 134 " --> pdb=" O   ILE C 140 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   LEU C 142 " --> pdb=" O   ILE C 132 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   ILE C 117 " --> pdb=" O   ALA C 129 " (cutoff:3.500A)
      removed outlier: 8.616A  pdb=" N   LEU C 131 " --> pdb=" O   GLN C 115 " (cutoff:3.500A)
      removed outlier: 11.399A  pdb=" N   GLN C 115 " --> pdb=" O   LEU C 131 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   GLU C  59 " --> pdb=" O   GLN C 115 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   ILE C 117 " --> pdb=" O   ARG C  57 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   ARG C  57 " --> pdb=" O   ILE C 117 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   ILE C 119 " --> pdb=" O   SER C  55 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   SER C  55 " --> pdb=" O   ILE C 119 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 155 through 156
      removed outlier: 7.263A  pdb=" N   ALA C 155 " --> pdb=" O   LEU C 225 " (cutoff:3.500A)
      removed outlier: 8.149A  pdb=" N   GLY C 227 " --> pdb=" O   ALA C 155 " (cutoff:3.500A)
      removed outlier: 5.814A  pdb=" N   ASN C 229 " --> pdb=" O   ILE C 246 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   ILE C 246 " --> pdb=" O   ASN C 229 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA C 231 " --> pdb=" O   PHE C 244 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   GLN C 204 " --> pdb=" O   LEU C 189 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   LEU C 189 " --> pdb=" O   GLN C 204 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   LEU C 218 " --> pdb=" O   ILE C 226 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 275
      removed outlier: 6.597A  pdb=" N   THR C 274 " --> pdb=" O   VAL C 294 " (cutoff:3.500A)
      removed outlier: 5.407A  pdb=" N   VAL C 294 " --> pdb=" O   THR C 274 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 271 through 275
      removed outlier: 6.597A  pdb=" N   THR C 274 " --> pdb=" O   VAL C 294 " (cutoff:3.500A)
      removed outlier: 5.407A  pdb=" N   VAL C 294 " --> pdb=" O   THR C 274 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   GLY C 344 " --> pdb=" O   THR C 315 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   LEU C 317 " --> pdb=" O   LYS C 342 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   LYS C 342 " --> pdb=" O   LEU C 317 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 53 through 60
      removed outlier: 7.809A  pdb=" N   SER A  93 " --> pdb=" O   ASN A 107 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   ASN A 107 " --> pdb=" O   SER A  93 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   TYR A 103 " --> pdb=" O   ILE A  97 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ILE A 140 " --> pdb=" O   SER A 134 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   SER A 134 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   LEU A 142 " --> pdb=" O   ILE A 132 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   ILE A 117 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
      removed outlier: 8.623A  pdb=" N   LEU A 131 " --> pdb=" O   GLN A 115 " (cutoff:3.500A)
      removed outlier: 11.749A  pdb=" N   GLN A 115 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   GLU A  59 " --> pdb=" O   GLN A 115 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   ILE A 117 " --> pdb=" O   ARG A  57 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ARG A  57 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   ILE A 119 " --> pdb=" O   SER A  55 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   SER A  55 " --> pdb=" O   ILE A 119 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'G' and resid 30 through 31
      removed outlier: 3.752A  pdb=" N   ILE A 232 " --> pdb=" O   UNK G  30 " (cutoff:3.500A)
      removed outlier: 5.797A  pdb=" N   ASN A 229 " --> pdb=" O   ILE A 246 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   ILE A 246 " --> pdb=" O   ASN A 229 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   GLN A 204 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 5.736A  pdb=" N   LEU A 189 " --> pdb=" O   GLN A 204 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   LEU A 218 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 267 through 268
      removed outlier: 3.646A  pdb=" N   LEU A 268 " --> pdb=" O   ASP A 359 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 271 through 275
      removed outlier: 6.818A  pdb=" N   LYS A 272 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 271 through 275
      removed outlier: 6.818A  pdb=" N   LYS A 272 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   GLY A 344 " --> pdb=" O   THR A 315 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   LEU A 317 " --> pdb=" O   LYS A 342 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   LYS A 342 " --> pdb=" O   LEU A 317 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 53 through 60
      removed outlier: 6.525A  pdb=" N   TYR B 103 " --> pdb=" O   ILE B  97 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   ILE B 140 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   SER B 134 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   LEU B 142 " --> pdb=" O   ILE B 132 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   ILE B 117 " --> pdb=" O   ALA B 129 " (cutoff:3.500A)
      removed outlier: 8.837A  pdb=" N   LEU B 131 " --> pdb=" O   GLN B 115 " (cutoff:3.500A)
      removed outlier: 11.671A  pdb=" N   GLN B 115 " --> pdb=" O   LEU B 131 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 167 through 172
      removed outlier: 5.345A  pdb=" N   PHE B 202 " --> pdb=" O   GLY B 190 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   PHE B 244 " --> pdb=" O   THR B 230 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   LEU B 218 " --> pdb=" O   ILE B 226 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 267 through 268
      removed outlier: 3.588A  pdb=" N   ASP B 359 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 271 through 275
      removed outlier: 6.693A  pdb=" N   THR B 274 " --> pdb=" O   VAL B 294 " (cutoff:3.500A)
      removed outlier: 5.426A  pdb=" N   VAL B 294 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 271 through 275
      removed outlier: 6.693A  pdb=" N   THR B 274 " --> pdb=" O   VAL B 294 " (cutoff:3.500A)
      removed outlier: 5.426A  pdb=" N   VAL B 294 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   GLY B 344 " --> pdb=" O   THR B 315 " (cutoff:3.500A)
      removed outlier: 4.942A  pdb=" N   LEU B 317 " --> pdb=" O   LYS B 342 " (cutoff:3.500A)
      removed outlier: 7.353A  pdb=" N   LYS B 342 " --> pdb=" O   LEU B 317 " (cutoff:3.500A)

    334 hydrogen bonds defined for protein.
    870 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: 2.58

  Time building geometry restraints manager: 2.36 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: 1945
        1.33 -     1.45: 1487
        1.45 -     1.57: 5197
        1.57 -     1.69: 0
        1.69 -     1.81: 34
  Bond restraints: 8663
  Sorted by residual:
  bond pdb=" N   ILE B 232 "
       pdb=" CA  ILE B 232 "
    ideal  model  delta    sigma   weight residual
    1.458  1.500 -0.042 1.08e-02 8.57e+03 1.52e+01
  bond pdb=" N   ILE D 443 "
       pdb=" CA  ILE D 443 "
    ideal  model  delta    sigma   weight residual
    1.459  1.507 -0.048 1.25e-02 6.40e+03 1.49e+01
  bond pdb=" N   ILE F 443 "
       pdb=" CA  ILE F 443 "
    ideal  model  delta    sigma   weight residual
    1.459  1.506 -0.047 1.25e-02 6.40e+03 1.43e+01
  bond pdb=" N   VAL F 444 "
       pdb=" CA  VAL F 444 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.25e-02 6.40e+03 9.31e+00
  bond pdb=" N   ILE E 443 "
       pdb=" CA  ILE E 443 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.25e-02 6.40e+03 9.25e+00
  ... (remaining 8658 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.14: 11574
        3.14 -     6.28: 110
        6.28 -     9.42: 8
        9.42 -    12.56: 1
       12.56 -    15.70: 3
  Bond angle restraints: 11696
  Sorted by residual:
  angle pdb=" C   ILE D 438 "
        pdb=" N   ILE D 439 "
        pdb=" CA  ILE D 439 "
      ideal   model   delta    sigma   weight residual
     122.93  115.75    7.18 1.31e+00 5.83e-01 3.00e+01
  angle pdb=" N   UNK G  29 "
        pdb=" CA  UNK G  29 "
        pdb=" C   UNK G  29 "
      ideal   model   delta    sigma   weight residual
     110.74   95.04   15.70 3.00e+00 1.11e-01 2.74e+01
  angle pdb=" N   UNK G  30 "
        pdb=" CA  UNK G  30 "
        pdb=" C   UNK G  30 "
      ideal   model   delta    sigma   weight residual
     110.74   97.52   13.22 3.00e+00 1.11e-01 1.94e+01
  angle pdb=" CA  LEU B 233 "
        pdb=" C   LEU B 233 "
        pdb=" O   LEU B 233 "
      ideal   model   delta    sigma   weight residual
     120.70  115.99    4.71 1.08e+00 8.57e-01 1.90e+01
  angle pdb=" N   UNK G  33 "
        pdb=" CA  UNK G  33 "
        pdb=" C   UNK G  33 "
      ideal   model   delta    sigma   weight residual
     110.74  123.52  -12.78 3.00e+00 1.11e-01 1.82e+01
  ... (remaining 11691 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 4579
       17.54 -    35.07: 504
       35.07 -    52.61: 161
       52.61 -    70.14: 48
       70.14 -    87.68: 15
  Dihedral angle restraints: 5307
    sinusoidal: 2032
      harmonic: 3275
  Sorted by residual:
  dihedral pdb=" CA  UNK G  33 "
           pdb=" C   UNK G  33 "
           pdb=" N   UNK G  34 "
           pdb=" CA  UNK G  34 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.02  -24.98     0      5.00e+00 4.00e-02 2.50e+01
  dihedral pdb=" CD  ARG D 445 "
           pdb=" NE  ARG D 445 "
           pdb=" CZ  ARG D 445 "
           pdb=" NH1 ARG D 445 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   36.07  -36.07     1      1.00e+01 1.00e-02 1.84e+01
  dihedral pdb=" CA  ASN A 201 "
           pdb=" C   ASN A 201 "
           pdb=" N   PHE A 202 "
           pdb=" CA  PHE A 202 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.60  -20.40     0      5.00e+00 4.00e-02 1.66e+01
  ... (remaining 5304 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 1280
       0.095 -    0.189: 127
       0.189 -    0.284: 4
       0.284 -    0.378: 2
       0.378 -    0.473: 1
  Chirality restraints: 1414
  Sorted by residual:
  chirality pdb=" CA  UNK G  33 "
            pdb=" N   UNK G  33 "
            pdb=" C   UNK G  33 "
            pdb=" CB  UNK G  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.52    2.05    0.47 2.00e-01 2.50e+01 5.58e+00
  chirality pdb=" CB  ILE B 111 "
            pdb=" CA  ILE B 111 "
            pdb=" CG1 ILE B 111 "
            pdb=" CG2 ILE B 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.45e+00
  chirality pdb=" CB  VAL D 444 "
            pdb=" CA  VAL D 444 "
            pdb=" CG1 VAL D 444 "
            pdb=" CG2 VAL D 444 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.31e+00
  ... (remaining 1411 not shown)

  Planarity restraints: 1539
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 445 "    0.638 9.50e-02 1.11e+02   2.86e-01 4.99e+01
        pdb=" NE  ARG D 445 "   -0.038 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 445 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 445 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 445 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 336 "    0.065 5.00e-02 4.00e+02   9.75e-02 1.52e+01
        pdb=" N   PRO B 337 "   -0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO B 337 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO B 337 "    0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE E 443 "   -0.013 2.00e-02 2.50e+03   2.56e-02 6.55e+00
        pdb=" C   ILE E 443 "    0.044 2.00e-02 2.50e+03
        pdb=" O   ILE E 443 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   VAL E 444 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1536 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 334
        2.72 -     3.26: 7630
        3.26 -     3.81: 12822
        3.81 -     4.35: 16367
        4.35 -     4.90: 28390
  Nonbonded interactions: 65543
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS C 116 "
            pdb=" OD1 ASP C 128 "
     model   vdw
     2.171 3.120
  nonbonded pdb=" OE2 GLU C 275 "
            pdb=" OG  SER C 324 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OG  SER C 149 "
            pdb=" NZ  LYS C 150 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" O   GLY B 198 "
            pdb=" NH1 ARG B 329 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" OE1 GLU A 275 "
            pdb=" OG  SER A 324 "
     model   vdw
     2.310 3.040
  ... (remaining 65538 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'E' and (resid 365 through 449 or resid 451 through 452))
  selection = (chain 'F' and (resid 365 through 449 or resid 451 through 452))
}
ncs_group {
  reference = (chain 'G' and resid 29 through 35)
  selection = chain 'I'
}

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:             3.180
  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:          0.410
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     23.400
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7150
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      :  0.005   0.074   8663  Z= 0.327
  Angle     :  0.816  15.696  11696  Z= 0.464
  Chirality :  0.054   0.473   1414
  Planarity :  0.010   0.286   1539
  Dihedral  : 17.673  87.678   3213
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  2.26 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 23.56 %
    Favored  : 72.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.24), residues: 1148
  helix:  0.21 (0.38), residues: 195
  sheet:  0.27 (0.28), residues: 324
  loop : -0.44 (0.24), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS C 109 
 PHE   0.013   0.002   PHE C 127 
 TYR   0.008   0.002   TYR E 451 
 ARG   0.012   0.001   ARG D 419 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 103
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 32
  outliers final: 15
  residues processed: 128
  average time/residue: 1.1506
  time to fit residues: 158.5044
Evaluate side-chains
  76 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  443 ILE
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  275 GLU
Chi-restraints excluded: chain C residue  334 THR
Chi-restraints excluded: chain A residue  118 SER
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  303 SER
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  334 THR
Chi-restraints excluded: chain B residue  339 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    0.9980
   chunk 87 optimal weight:    0.0970
   chunk 48 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.7578

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

Flipped N/Q/H residues before XYZ refinement:
D 442 GLN
A 107 ASN
A 173 ASN
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.150866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.080388 restraints weight = 12999.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 3.20
r_work: 0.2824 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8663  Z= 0.209
  Angle     :  0.570   7.464  11696  Z= 0.293
  Chirality :  0.046   0.213   1414
  Planarity :  0.004   0.058   1539
  Dihedral  :  5.182  53.628   1246
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.61 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 22.46 %
    Favored  : 72.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.25), residues: 1148
  helix:  0.83 (0.40), residues: 195
  sheet:  0.45 (0.29), residues: 313
  loop : -0.28 (0.25), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.002   HIS A 109 
 PHE   0.010   0.001   PHE C 127 
 TYR   0.005   0.001   TYR E 451 
 ARG   0.007   0.000   ARG D 419 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 74
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  445 ARG cc_start: 0.5360 (ptp-110) cc_final: 0.5013 (tpm-80)
REVERT: F  428 MET cc_start: 0.7175 (ttp) cc_final: 0.6608 (pp-130)
REVERT: C  128 ASP cc_start: 0.8383 (m-30) cc_final: 0.7892 (t70)
REVERT: A  282 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7757 (ttmt)
REVERT: A  331 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7702 (mtt90)
REVERT: B  139 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8227 (t0)
  outliers start: 43
  outliers final: 11
  residues processed: 105
  average time/residue: 1.0058
  time to fit residues: 114.4717
Evaluate side-chains
  77 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  443 ILE
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain F residue  441 LEU
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  282 LYS
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  331 ARG
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  294 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 109 optimal weight:    0.9990
   chunk 86 optimal weight:    0.6980
   chunk 87 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 104 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 111 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
C 213 ASN
A 107 ASN
A 173 ASN
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 112 ASN
** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.148531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.078154 restraints weight = 13279.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 3.23
r_work: 0.2785 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8663  Z= 0.258
  Angle     :  0.556   6.849  11696  Z= 0.286
  Chirality :  0.046   0.226   1414
  Planarity :  0.004   0.047   1539
  Dihedral  :  4.783  56.147   1232
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.44 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 23.89 %
    Favored  : 72.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.25), residues: 1148
  helix:  1.08 (0.39), residues: 195
  sheet:  0.32 (0.28), residues: 323
  loop : -0.19 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.002   HIS B 109 
 PHE   0.011   0.001   PHE C 127 
 TYR   0.006   0.001   TYR F 451 
 ARG   0.008   0.001   ARG E 445 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 68
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
REVERT: F  428 MET cc_start: 0.7190 (ttp) cc_final: 0.6569 (pp-130)
REVERT: C  128 ASP cc_start: 0.8454 (m-30) cc_final: 0.7924 (t70)
REVERT: C  275 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8064 (mm-30)
REVERT: A  331 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7686 (mtt90)
REVERT: B  139 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.7919 (t0)
  outliers start: 34
  outliers final: 13
  residues processed: 88
  average time/residue: 1.0437
  time to fit residues: 99.5133
Evaluate side-chains
  73 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  372 THR
Chi-restraints excluded: chain D residue  443 ILE
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain C residue   45 MET
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  275 GLU
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  331 ARG
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  294 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 13 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 50 optimal weight:   10.0000
   chunk 15 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 16 optimal weight:    4.9990
   chunk 95 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 107 ASN
A 120 GLN
A 173 ASN
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.148032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.077435 restraints weight = 13284.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 3.26
r_work: 0.2781 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8663  Z= 0.259
  Angle     :  0.552   8.176  11696  Z= 0.283
  Chirality :  0.046   0.209   1414
  Planarity :  0.004   0.040   1539
  Dihedral  :  4.706  59.624   1231
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.26 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 24.78 %
    Favored  : 71.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.25), residues: 1148
  helix:  1.18 (0.39), residues: 195
  sheet:  0.32 (0.28), residues: 330
  loop : -0.00 (0.26), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 109 
 PHE   0.011   0.001   PHE C 127 
 TYR   0.004   0.001   TYR F 451 
 ARG   0.005   0.000   ARG C 331 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 60
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
REVERT: E  370 MET cc_start: 0.6051 (pmm) cc_final: 0.5487 (pmm)
REVERT: F  428 MET cc_start: 0.7199 (ttp) cc_final: 0.6558 (pp-130)
REVERT: C  275 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7984 (mm-30)
REVERT: A  331 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7683 (mtt90)
REVERT: B  139 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.7992 (t0)
  outliers start: 33
  outliers final: 16
  residues processed: 83
  average time/residue: 1.0214
  time to fit residues: 91.9031
Evaluate side-chains
  75 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 56
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  372 THR
Chi-restraints excluded: chain D residue  443 ILE
Chi-restraints excluded: chain E residue  449 SER
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain C residue   45 MET
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  275 GLU
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  331 ARG
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  294 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 21 optimal weight:   10.0000
   chunk 97 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 18 optimal weight:   30.0000
   chunk 49 optimal weight:   10.0000
   chunk 58 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9980
   chunk 17 optimal weight:   20.0000
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 107 ASN
A 173 ASN
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.146579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.076529 restraints weight = 13223.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 3.24
r_work: 0.2772 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   8663  Z= 0.333
  Angle     :  0.575   8.977  11696  Z= 0.296
  Chirality :  0.047   0.213   1414
  Planarity :  0.004   0.037   1539
  Dihedral  :  4.823  59.020   1231
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.96 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 24.00 %
    Favored  : 71.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.25), residues: 1148
  helix:  1.21 (0.39), residues: 195
  sheet:  0.27 (0.28), residues: 337
  loop : -0.12 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.002   HIS B 109 
 PHE   0.014   0.001   PHE C 127 
 TYR   0.007   0.001   TYR F 451 
 ARG   0.006   0.000   ARG E 445 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 59
  time to evaluate  : 0.919 
Fit side-chains
REVERT: F  428 MET cc_start: 0.7158 (ttp) cc_final: 0.6477 (pp-130)
REVERT: C  128 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8285 (p0)
REVERT: A  331 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7711 (mtt90)
REVERT: B  139 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8055 (t0)
  outliers start: 39
  outliers final: 17
  residues processed: 86
  average time/residue: 0.9896
  time to fit residues: 92.3464
Evaluate side-chains
  81 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 61
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  372 THR
Chi-restraints excluded: chain D residue  443 ILE
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  128 ASP
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  331 ARG
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  339 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 17 optimal weight:   30.0000
   chunk 54 optimal weight:    7.9990
   chunk 98 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 79 optimal weight:    8.9990
   chunk 73 optimal weight:    0.9980
   chunk 21 optimal weight:   20.0000
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 107 ASN
A 173 ASN
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.147967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.079614 restraints weight = 13077.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 3.05
r_work: 0.2863 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8663  Z= 0.244
  Angle     :  0.557   9.625  11696  Z= 0.282
  Chirality :  0.046   0.201   1414
  Planarity :  0.003   0.034   1539
  Dihedral  :  4.637  59.472   1231
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.44 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 24.89 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.26), residues: 1148
  helix:  1.34 (0.39), residues: 195
  sheet:  0.33 (0.28), residues: 338
  loop : -0.00 (0.26), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 109 
 PHE   0.011   0.001   PHE C 127 
 TYR   0.005   0.001   TYR F 451 
 ARG   0.006   0.000   ARG E 445 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 65
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
REVERT: D  421 ARG cc_start: 0.4889 (tpp80) cc_final: 0.4250 (tpp-160)
REVERT: E  370 MET cc_start: 0.5601 (pmm) cc_final: 0.5133 (pmm)
REVERT: F  439 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7169 (tp)
REVERT: C  149 SER cc_start: 0.8501 (OUTLIER) cc_final: 0.8143 (p)
REVERT: A  331 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7839 (mtt90)
REVERT: B  139 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8078 (t0)
  outliers start: 35
  outliers final: 17
  residues processed: 89
  average time/residue: 1.0659
  time to fit residues: 102.7005
Evaluate side-chains
  83 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 62
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  372 THR
Chi-restraints excluded: chain D residue  443 ILE
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain F residue  439 ILE
Chi-restraints excluded: chain C residue   45 MET
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  331 ARG
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  339 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 91 optimal weight:    0.2980
   chunk 9 optimal weight:    1.9990
   chunk 17 optimal weight:   30.0000
   chunk 21 optimal weight:   20.0000
   chunk 49 optimal weight:    5.9990
   chunk 71 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 111 optimal weight:    4.9990
   chunk 89 optimal weight:    0.8980
   chunk 77 optimal weight:    3.9990
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
A 107 ASN
A 173 ASN
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.146875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.077048 restraints weight = 13275.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 3.21
r_work: 0.2767 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8663  Z= 0.314
  Angle     :  0.593  10.277  11696  Z= 0.299
  Chirality :  0.047   0.198   1414
  Planarity :  0.003   0.035   1539
  Dihedral  :  4.764  59.324   1231
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.05 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 25.44 %
    Favored  : 71.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.25), residues: 1148
  helix:  1.39 (0.39), residues: 195
  sheet:  0.32 (0.28), residues: 338
  loop : -0.08 (0.26), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.002   HIS B 109 
 PHE   0.012   0.001   PHE C 127 
 TYR   0.007   0.001   TYR F 451 
 ARG   0.006   0.000   ARG E 445 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 63
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
REVERT: D  421 ARG cc_start: 0.4746 (tpp80) cc_final: 0.4126 (tpp-160)
REVERT: C  128 ASP cc_start: 0.8231 (p0) cc_final: 0.7713 (p0)
REVERT: C  135 ASP cc_start: 0.7837 (t70) cc_final: 0.7222 (t0)
REVERT: C  149 SER cc_start: 0.8405 (OUTLIER) cc_final: 0.8019 (p)
REVERT: C  282 LYS cc_start: 0.9079 (mtpt) cc_final: 0.8836 (mttp)
REVERT: A  331 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7668 (mtt90)
REVERT: B  139 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8013 (t0)
  outliers start: 32
  outliers final: 22
  residues processed: 86
  average time/residue: 0.9591
  time to fit residues: 89.7906
Evaluate side-chains
  86 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 61
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  372 THR
Chi-restraints excluded: chain D residue  443 ILE
Chi-restraints excluded: chain E residue  422 VAL
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain F residue  439 ILE
Chi-restraints excluded: chain F residue  441 LEU
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  331 ARG
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  339 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 96 optimal weight:    0.8980
   chunk 86 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 67 optimal weight:    0.4980
   chunk 112 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9980
   chunk 109 optimal weight:    5.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 107 ASN
A 173 ASN
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.148165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.078722 restraints weight = 13259.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 3.21
r_work: 0.2797 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.3139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8663  Z= 0.207
  Angle     :  0.563  11.116  11696  Z= 0.281
  Chirality :  0.045   0.185   1414
  Planarity :  0.003   0.033   1539
  Dihedral  :  4.504  59.615   1231
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.18 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 25.55 %
    Favored  : 71.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.26), residues: 1148
  helix:  1.57 (0.39), residues: 195
  sheet:  0.37 (0.29), residues: 338
  loop :  0.05 (0.26), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 109 
 PHE   0.009   0.001   PHE C 127 
 TYR   0.003   0.001   TYR D 451 
 ARG   0.007   0.000   ARG E 445 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 67
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
REVERT: D  421 ARG cc_start: 0.4848 (tpp80) cc_final: 0.4080 (tpp-160)
REVERT: E  370 MET cc_start: 0.5418 (pmm) cc_final: 0.5094 (pmm)
REVERT: C  128 ASP cc_start: 0.8244 (p0) cc_final: 0.7759 (p0)
REVERT: C  135 ASP cc_start: 0.7820 (t70) cc_final: 0.7233 (t0)
REVERT: C  149 SER cc_start: 0.8382 (OUTLIER) cc_final: 0.8000 (p)
REVERT: C  282 LYS cc_start: 0.9077 (mtpt) cc_final: 0.8832 (mttp)
REVERT: A  331 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7688 (mtt90)
REVERT: B  139 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.7912 (t0)
  outliers start: 30
  outliers final: 16
  residues processed: 88
  average time/residue: 0.9399
  time to fit residues: 90.2859
Evaluate side-chains
  80 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  372 THR
Chi-restraints excluded: chain D residue  443 ILE
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain F residue  439 ILE
Chi-restraints excluded: chain F residue  441 LEU
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  331 ARG
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  339 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 18 optimal weight:   20.0000
   chunk 99 optimal weight:    6.9990
   chunk 69 optimal weight:    0.1980
   chunk 24 optimal weight:   20.0000
   chunk 44 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 93 optimal weight:    1.9990
   chunk 39 optimal weight:    0.3980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 107 ASN
A 173 ASN
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.147948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.078619 restraints weight = 13249.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.2983 rms_B_bonded: 3.21
r_work: 0.2798 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.3229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8663  Z= 0.210
  Angle     :  0.572  11.773  11696  Z= 0.285
  Chirality :  0.046   0.191   1414
  Planarity :  0.003   0.034   1539
  Dihedral  :  4.464  59.992   1231
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.35 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 25.55 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.26), residues: 1148
  helix:  1.67 (0.39), residues: 195
  sheet:  0.38 (0.29), residues: 338
  loop :  0.10 (0.27), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 109 
 PHE   0.010   0.001   PHE C 127 
 TYR   0.004   0.001   TYR F 451 
 ARG   0.009   0.000   ARG E 445 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 63
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
REVERT: D  421 ARG cc_start: 0.4867 (tpp80) cc_final: 0.4220 (tpp-160)
REVERT: C  128 ASP cc_start: 0.8260 (p0) cc_final: 0.7817 (p0)
REVERT: C  135 ASP cc_start: 0.7861 (t70) cc_final: 0.7306 (t0)
REVERT: C  149 SER cc_start: 0.8421 (OUTLIER) cc_final: 0.8058 (p)
REVERT: C  282 LYS cc_start: 0.9046 (mtpt) cc_final: 0.8796 (mttp)
REVERT: A  331 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7713 (mtt90)
REVERT: B  139 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.7954 (t0)
  outliers start: 29
  outliers final: 20
  residues processed: 82
  average time/residue: 0.9651
  time to fit residues: 86.1293
Evaluate side-chains
  85 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 62
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  372 THR
Chi-restraints excluded: chain D residue  443 ILE
Chi-restraints excluded: chain E residue  449 SER
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain F residue  372 THR
Chi-restraints excluded: chain F residue  439 ILE
Chi-restraints excluded: chain F residue  441 LEU
Chi-restraints excluded: chain C residue   45 MET
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  331 ARG
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  339 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 92 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 111 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0570
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.1302

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

Flipped N/Q/H residues before XYZ refinement:
A 107 ASN
A 173 ASN
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.147438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.077332 restraints weight = 13216.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 3.22
r_work: 0.2783 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.3288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8663  Z= 0.264
  Angle     :  0.590  12.311  11696  Z= 0.293
  Chirality :  0.046   0.202   1414
  Planarity :  0.003   0.034   1539
  Dihedral  :  4.606  59.468   1231
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.53 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 26.00 %
    Favored  : 71.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.26), residues: 1148
  helix:  1.58 (0.39), residues: 195
  sheet:  0.16 (0.28), residues: 353
  loop :  0.17 (0.27), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 109 
 PHE   0.012   0.001   PHE C 127 
 TYR   0.006   0.001   TYR F 451 
 ARG   0.008   0.000   ARG E 445 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 63
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
REVERT: E  428 MET cc_start: 0.5989 (mmm) cc_final: 0.5615 (mtt)
REVERT: C  128 ASP cc_start: 0.8352 (p0) cc_final: 0.7876 (p0)
REVERT: C  135 ASP cc_start: 0.7954 (t70) cc_final: 0.7369 (t0)
REVERT: C  149 SER cc_start: 0.8439 (OUTLIER) cc_final: 0.8083 (p)
REVERT: C  282 LYS cc_start: 0.9052 (mtpt) cc_final: 0.8822 (mttt)
REVERT: A  331 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7734 (mtt90)
REVERT: B  139 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8021 (t0)
  outliers start: 27
  outliers final: 19
  residues processed: 81
  average time/residue: 1.1537
  time to fit residues: 102.3644
Evaluate side-chains
  82 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 60
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  372 THR
Chi-restraints excluded: chain D residue  443 ILE
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain F residue  372 THR
Chi-restraints excluded: chain F residue  439 ILE
Chi-restraints excluded: chain F residue  441 LEU
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  331 ARG
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  339 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 100 optimal weight:    0.8980
   chunk 16 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 13 optimal weight:    8.9990
   chunk 63 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0870
   chunk 42 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.9560

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

Flipped N/Q/H residues before XYZ refinement:
A 107 ASN
A 173 ASN
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.147619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.078180 restraints weight = 13314.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.2983 rms_B_bonded: 3.22
r_work: 0.2797 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.3361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8663  Z= 0.230
  Angle     :  0.576  12.352  11696  Z= 0.286
  Chirality :  0.046   0.198   1414
  Planarity :  0.003   0.036   1539
  Dihedral  :  4.487  57.994   1231
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.18 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 25.88 %
    Favored  : 71.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.26), residues: 1148
  helix:  1.71 (0.39), residues: 195
  sheet:  0.20 (0.28), residues: 353
  loop :  0.19 (0.27), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.002   HIS C 109 
 PHE   0.010   0.001   PHE C 127 
 TYR   0.004   0.001   TYR F 451 
 ARG   0.009   0.000   ARG E 445 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8127.74 seconds
wall clock time: 139 minutes 39.92 seconds (8379.92 seconds total)