Starting phenix.real_space_refine
on Mon Oct 14 19:29:25 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8own_17240/10_2024/8own_17240.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8own_17240/10_2024/8own_17240.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8own_17240/10_2024/8own_17240.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8own_17240/10_2024/8own_17240.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8own_17240/10_2024/8own_17240.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8own_17240/10_2024/8own_17240.cif"
  }
  resolution = 3.26
  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=   0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      6      9.91       5
     S      96      5.16       5
     C   11844      2.51       5
     N    3330      2.21       5
     O    3528      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.08s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib"
  Total number of atoms: 18804
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 410, 3133
          Classifications: {'peptide': 410}
          Link IDs: {'PTRANS': 16, 'TRANS': 393}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 8.34, per 1000 atoms: 0.44
  Number of scatterers: 18804
  At special positions: 0
  Unit cell: (116.96, 116.1, 124.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      6     19.99
     S      96     16.00
     O    3528      8.00
     N    3330      7.00
     C   11844      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: 5.04
  Conformation dependent library (CDL) restraints added in 2.6 seconds
  

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4416

  Finding SS restraints...
    Secondary structure from input PDB file:
      108 helices and 9 sheets defined
      57.6% alpha, 13.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 19
      removed outlier: 3.704A  pdb=" N   ALA A   6 " --> pdb=" O   ASN A   2 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   THR A   7 " --> pdb=" O   ALA A   3 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ASN A   8 " --> pdb=" O   LEU A   4 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 30
    Processing helix  chain 'A' and resid 76 through 95
    Processing helix  chain 'A' and resid 113 through 128
    Processing helix  chain 'A' and resid 129 through 132
      removed outlier: 3.843A  pdb=" N   ILE A 132 " --> pdb=" O   HIS A 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 129 through 132'
    Processing helix  chain 'A' and resid 146 through 162
      removed outlier: 3.563A  pdb=" N   MET A 150 " --> pdb=" O   ASN A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 168
      removed outlier: 4.259A  pdb=" N   VAL A 168 " --> pdb=" O   PRO A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 176
    Processing helix  chain 'A' and resid 183 through 200
      removed outlier: 3.836A  pdb=" N   TYR A 200 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 229
    Processing helix  chain 'A' and resid 249 through 261
      removed outlier: 3.834A  pdb=" N   LYS A 255 " --> pdb=" O   ASN A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 280
    Processing helix  chain 'A' and resid 295 through 300
      removed outlier: 4.114A  pdb=" N   GLY A 300 " --> pdb=" O   LYS A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 327
    Processing helix  chain 'A' and resid 332 through 337
      removed outlier: 3.867A  pdb=" N   ASN A 337 " --> pdb=" O   ASP A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 354
    Processing helix  chain 'A' and resid 358 through 385
    Processing helix  chain 'A' and resid 387 through 408
      removed outlier: 3.583A  pdb=" N   GLY A 408 " --> pdb=" O   THR A 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 19
      removed outlier: 4.390A  pdb=" N   THR B   7 " --> pdb=" O   ALA B   3 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ASN B   8 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 30
    Processing helix  chain 'B' and resid 76 through 95
    Processing helix  chain 'B' and resid 113 through 128
    Processing helix  chain 'B' and resid 129 through 132
      removed outlier: 3.843A  pdb=" N   ILE B 132 " --> pdb=" O   HIS B 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 129 through 132'
    Processing helix  chain 'B' and resid 146 through 162
      removed outlier: 3.562A  pdb=" N   MET B 150 " --> pdb=" O   ASN B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 168
      removed outlier: 4.259A  pdb=" N   VAL B 168 " --> pdb=" O   PRO B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 176
    Processing helix  chain 'B' and resid 183 through 200
      removed outlier: 3.836A  pdb=" N   TYR B 200 " --> pdb=" O   LEU B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 229
    Processing helix  chain 'B' and resid 249 through 261
      removed outlier: 3.834A  pdb=" N   LYS B 255 " --> pdb=" O   ASN B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 280
    Processing helix  chain 'B' and resid 295 through 300
      removed outlier: 4.114A  pdb=" N   GLY B 300 " --> pdb=" O   LYS B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 327
    Processing helix  chain 'B' and resid 332 through 337
      removed outlier: 3.866A  pdb=" N   ASN B 337 " --> pdb=" O   ASP B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 354
    Processing helix  chain 'B' and resid 358 through 385
    Processing helix  chain 'B' and resid 387 through 408
      removed outlier: 3.583A  pdb=" N   GLY B 408 " --> pdb=" O   THR B 404 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3 through 19
      removed outlier: 4.391A  pdb=" N   THR C   7 " --> pdb=" O   ALA C   3 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ASN C   8 " --> pdb=" O   LEU C   4 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 30
    Processing helix  chain 'C' and resid 76 through 95
    Processing helix  chain 'C' and resid 113 through 128
    Processing helix  chain 'C' and resid 129 through 132
      removed outlier: 3.843A  pdb=" N   ILE C 132 " --> pdb=" O   HIS C 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 129 through 132'
    Processing helix  chain 'C' and resid 146 through 162
      removed outlier: 3.564A  pdb=" N   MET C 150 " --> pdb=" O   ASN C 146 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 164 through 168
      removed outlier: 4.259A  pdb=" N   VAL C 168 " --> pdb=" O   PRO C 165 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 176
    Processing helix  chain 'C' and resid 183 through 200
      removed outlier: 3.835A  pdb=" N   TYR C 200 " --> pdb=" O   LEU C 196 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 215 through 229
    Processing helix  chain 'C' and resid 249 through 261
      removed outlier: 3.834A  pdb=" N   LYS C 255 " --> pdb=" O   ASN C 251 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 276 through 280
    Processing helix  chain 'C' and resid 295 through 300
      removed outlier: 4.114A  pdb=" N   GLY C 300 " --> pdb=" O   LYS C 296 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 316 through 327
    Processing helix  chain 'C' and resid 332 through 337
      removed outlier: 3.866A  pdb=" N   ASN C 337 " --> pdb=" O   ASP C 333 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 338 through 354
    Processing helix  chain 'C' and resid 358 through 385
    Processing helix  chain 'C' and resid 387 through 408
      removed outlier: 3.583A  pdb=" N   GLY C 408 " --> pdb=" O   THR C 404 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 19
      removed outlier: 4.390A  pdb=" N   THR D   7 " --> pdb=" O   ALA D   3 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ASN D   8 " --> pdb=" O   LEU D   4 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 21 through 30
    Processing helix  chain 'D' and resid 76 through 95
    Processing helix  chain 'D' and resid 113 through 128
    Processing helix  chain 'D' and resid 129 through 132
      removed outlier: 3.843A  pdb=" N   ILE D 132 " --> pdb=" O   HIS D 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 129 through 132'
    Processing helix  chain 'D' and resid 146 through 162
      removed outlier: 3.563A  pdb=" N   MET D 150 " --> pdb=" O   ASN D 146 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 164 through 168
      removed outlier: 4.257A  pdb=" N   VAL D 168 " --> pdb=" O   PRO D 165 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 172 through 176
    Processing helix  chain 'D' and resid 183 through 200
      removed outlier: 3.836A  pdb=" N   TYR D 200 " --> pdb=" O   LEU D 196 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 215 through 229
    Processing helix  chain 'D' and resid 249 through 261
      removed outlier: 3.834A  pdb=" N   LYS D 255 " --> pdb=" O   ASN D 251 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 276 through 280
    Processing helix  chain 'D' and resid 295 through 300
      removed outlier: 4.114A  pdb=" N   GLY D 300 " --> pdb=" O   LYS D 296 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 316 through 327
    Processing helix  chain 'D' and resid 332 through 337
      removed outlier: 3.867A  pdb=" N   ASN D 337 " --> pdb=" O   ASP D 333 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 338 through 354
    Processing helix  chain 'D' and resid 358 through 385
    Processing helix  chain 'D' and resid 387 through 408
      removed outlier: 3.584A  pdb=" N   GLY D 408 " --> pdb=" O   THR D 404 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3 through 19
      removed outlier: 4.390A  pdb=" N   THR E   7 " --> pdb=" O   ALA E   3 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ASN E   8 " --> pdb=" O   LEU E   4 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 21 through 30
    Processing helix  chain 'E' and resid 76 through 95
    Processing helix  chain 'E' and resid 113 through 128
    Processing helix  chain 'E' and resid 129 through 132
      removed outlier: 3.843A  pdb=" N   ILE E 132 " --> pdb=" O   HIS E 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 129 through 132'
    Processing helix  chain 'E' and resid 146 through 162
      removed outlier: 3.563A  pdb=" N   MET E 150 " --> pdb=" O   ASN E 146 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 164 through 168
      removed outlier: 4.259A  pdb=" N   VAL E 168 " --> pdb=" O   PRO E 165 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 172 through 176
    Processing helix  chain 'E' and resid 183 through 200
      removed outlier: 3.837A  pdb=" N   TYR E 200 " --> pdb=" O   LEU E 196 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 215 through 229
    Processing helix  chain 'E' and resid 249 through 261
      removed outlier: 3.835A  pdb=" N   LYS E 255 " --> pdb=" O   ASN E 251 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 276 through 280
    Processing helix  chain 'E' and resid 295 through 300
      removed outlier: 4.114A  pdb=" N   GLY E 300 " --> pdb=" O   LYS E 296 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 316 through 327
    Processing helix  chain 'E' and resid 332 through 337
      removed outlier: 3.866A  pdb=" N   ASN E 337 " --> pdb=" O   ASP E 333 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 338 through 354
    Processing helix  chain 'E' and resid 358 through 385
    Processing helix  chain 'E' and resid 387 through 408
      removed outlier: 3.583A  pdb=" N   GLY E 408 " --> pdb=" O   THR E 404 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 3 through 19
      removed outlier: 4.390A  pdb=" N   THR F   7 " --> pdb=" O   ALA F   3 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ASN F   8 " --> pdb=" O   LEU F   4 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 21 through 30
    Processing helix  chain 'F' and resid 76 through 95
    Processing helix  chain 'F' and resid 113 through 128
    Processing helix  chain 'F' and resid 129 through 132
      removed outlier: 3.842A  pdb=" N   ILE F 132 " --> pdb=" O   HIS F 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 129 through 132'
    Processing helix  chain 'F' and resid 146 through 162
      removed outlier: 3.563A  pdb=" N   MET F 150 " --> pdb=" O   ASN F 146 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 164 through 168
      removed outlier: 4.258A  pdb=" N   VAL F 168 " --> pdb=" O   PRO F 165 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 172 through 176
    Processing helix  chain 'F' and resid 183 through 200
      removed outlier: 3.836A  pdb=" N   TYR F 200 " --> pdb=" O   LEU F 196 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 215 through 229
    Processing helix  chain 'F' and resid 249 through 261
      removed outlier: 3.834A  pdb=" N   LYS F 255 " --> pdb=" O   ASN F 251 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 276 through 280
    Processing helix  chain 'F' and resid 295 through 300
      removed outlier: 4.115A  pdb=" N   GLY F 300 " --> pdb=" O   LYS F 296 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 316 through 327
    Processing helix  chain 'F' and resid 332 through 337
      removed outlier: 3.866A  pdb=" N   ASN F 337 " --> pdb=" O   ASP F 333 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 338 through 354
    Processing helix  chain 'F' and resid 358 through 385
    Processing helix  chain 'F' and resid 387 through 408
      removed outlier: 3.583A  pdb=" N   GLY F 408 " --> pdb=" O   THR F 404 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 137 through 141
      removed outlier: 6.691A  pdb=" N   MET A  65 " --> pdb=" O   VAL A 138 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   ALA A 140 " --> pdb=" O   MET A  65 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   GLY A  67 " --> pdb=" O   ALA A 140 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   LYS A  66 " --> pdb=" O   ALA A 101 " (cutoff:3.500A)
      removed outlier: 7.826A  pdb=" N   GLY A 103 " --> pdb=" O   LYS A  66 " (cutoff:3.500A)
      removed outlier: 5.925A  pdb=" N   GLY A  68 " --> pdb=" O   GLY A 103 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   ILE A 105 " --> pdb=" O   GLY A  68 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   ARG A  70 " --> pdb=" O   ILE A 105 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   GLY A 100 " --> pdb=" O   HIS A  58 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   GLY D 100 " --> pdb=" O   HIS D  58 " (cutoff:3.500A)
      removed outlier: 5.907A  pdb=" N   LYS D  66 " --> pdb=" O   ALA D 101 " (cutoff:3.500A)
      removed outlier: 7.826A  pdb=" N   GLY D 103 " --> pdb=" O   LYS D  66 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   GLY D  68 " --> pdb=" O   GLY D 103 " (cutoff:3.500A)
      removed outlier: 7.858A  pdb=" N   ILE D 105 " --> pdb=" O   GLY D  68 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   ARG D  70 " --> pdb=" O   ILE D 105 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   MET D  65 " --> pdb=" O   VAL D 138 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   ALA D 140 " --> pdb=" O   MET D  65 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   GLY D  67 " --> pdb=" O   ALA D 140 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 271
      removed outlier: 7.798A  pdb=" N   PHE A 209 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   VAL A 235 " --> pdb=" O   PHE A 209 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   ILE A 211 " --> pdb=" O   VAL A 235 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   THR A 208 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   ILE A 286 " --> pdb=" O   THR A 208 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   VAL A 210 " --> pdb=" O   ILE A 286 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   ILE A 307 " --> pdb=" O   LEU A 331 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 137 through 141
      removed outlier: 6.692A  pdb=" N   MET B  65 " --> pdb=" O   VAL B 138 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   ALA B 140 " --> pdb=" O   MET B  65 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   GLY B  67 " --> pdb=" O   ALA B 140 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   LYS B  66 " --> pdb=" O   ALA B 101 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   GLY B 103 " --> pdb=" O   LYS B  66 " (cutoff:3.500A)
      removed outlier: 5.925A  pdb=" N   GLY B  68 " --> pdb=" O   GLY B 103 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   ILE B 105 " --> pdb=" O   GLY B  68 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   ARG B  70 " --> pdb=" O   ILE B 105 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   GLY B 100 " --> pdb=" O   HIS B  58 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   GLY E 100 " --> pdb=" O   HIS E  58 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   LYS E  66 " --> pdb=" O   ALA E 101 " (cutoff:3.500A)
      removed outlier: 7.826A  pdb=" N   GLY E 103 " --> pdb=" O   LYS E  66 " (cutoff:3.500A)
      removed outlier: 5.925A  pdb=" N   GLY E  68 " --> pdb=" O   GLY E 103 " (cutoff:3.500A)
      removed outlier: 7.858A  pdb=" N   ILE E 105 " --> pdb=" O   GLY E  68 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   ARG E  70 " --> pdb=" O   ILE E 105 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   MET E  65 " --> pdb=" O   VAL E 138 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   ALA E 140 " --> pdb=" O   MET E  65 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   GLY E  67 " --> pdb=" O   ALA E 140 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 270 through 271
      removed outlier: 7.798A  pdb=" N   PHE B 209 " --> pdb=" O   VAL B 233 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL B 235 " --> pdb=" O   PHE B 209 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   ILE B 211 " --> pdb=" O   VAL B 235 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   THR B 208 " --> pdb=" O   VAL B 284 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   ILE B 286 " --> pdb=" O   THR B 208 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   VAL B 210 " --> pdb=" O   ILE B 286 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   ILE B 307 " --> pdb=" O   LEU B 331 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 137 through 141
      removed outlier: 6.691A  pdb=" N   MET C  65 " --> pdb=" O   VAL C 138 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   ALA C 140 " --> pdb=" O   MET C  65 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   GLY C  67 " --> pdb=" O   ALA C 140 " (cutoff:3.500A)
      removed outlier: 5.907A  pdb=" N   LYS C  66 " --> pdb=" O   ALA C 101 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   GLY C 103 " --> pdb=" O   LYS C  66 " (cutoff:3.500A)
      removed outlier: 5.925A  pdb=" N   GLY C  68 " --> pdb=" O   GLY C 103 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   ILE C 105 " --> pdb=" O   GLY C  68 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   ARG C  70 " --> pdb=" O   ILE C 105 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   GLY C 100 " --> pdb=" O   HIS C  58 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   GLY F 100 " --> pdb=" O   HIS F  58 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   LYS F  66 " --> pdb=" O   ALA F 101 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   GLY F 103 " --> pdb=" O   LYS F  66 " (cutoff:3.500A)
      removed outlier: 5.924A  pdb=" N   GLY F  68 " --> pdb=" O   GLY F 103 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   ILE F 105 " --> pdb=" O   GLY F  68 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   ARG F  70 " --> pdb=" O   ILE F 105 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   MET F  65 " --> pdb=" O   VAL F 138 " (cutoff:3.500A)
      removed outlier: 7.647A  pdb=" N   ALA F 140 " --> pdb=" O   MET F  65 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   GLY F  67 " --> pdb=" O   ALA F 140 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 270 through 271
      removed outlier: 7.798A  pdb=" N   PHE C 209 " --> pdb=" O   VAL C 233 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   VAL C 235 " --> pdb=" O   PHE C 209 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   ILE C 211 " --> pdb=" O   VAL C 235 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   THR C 208 " --> pdb=" O   VAL C 284 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   ILE C 286 " --> pdb=" O   THR C 208 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   VAL C 210 " --> pdb=" O   ILE C 286 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   ILE C 307 " --> pdb=" O   LEU C 331 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 270 through 271
      removed outlier: 7.798A  pdb=" N   PHE D 209 " --> pdb=" O   VAL D 233 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   VAL D 235 " --> pdb=" O   PHE D 209 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   ILE D 211 " --> pdb=" O   VAL D 235 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   THR D 208 " --> pdb=" O   VAL D 284 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   ILE D 286 " --> pdb=" O   THR D 208 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   VAL D 210 " --> pdb=" O   ILE D 286 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   ILE D 307 " --> pdb=" O   LEU D 331 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 270 through 271
      removed outlier: 7.798A  pdb=" N   PHE E 209 " --> pdb=" O   VAL E 233 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   VAL E 235 " --> pdb=" O   PHE E 209 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   ILE E 211 " --> pdb=" O   VAL E 235 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   THR E 208 " --> pdb=" O   VAL E 284 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   ILE E 286 " --> pdb=" O   THR E 208 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   VAL E 210 " --> pdb=" O   ILE E 286 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   ILE E 307 " --> pdb=" O   LEU E 331 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 270 through 271
      removed outlier: 7.798A  pdb=" N   PHE F 209 " --> pdb=" O   VAL F 233 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   VAL F 235 " --> pdb=" O   PHE F 209 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   ILE F 211 " --> pdb=" O   VAL F 235 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   THR F 208 " --> pdb=" O   VAL F 284 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   ILE F 286 " --> pdb=" O   THR F 208 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   VAL F 210 " --> pdb=" O   ILE F 286 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   ILE F 307 " --> pdb=" O   LEU F 331 " (cutoff:3.500A)

    1086 hydrogen bonds defined for protein.
    3132 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: 6.47

  Time building geometry restraints manager: 5.73 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 6365
        1.34 -     1.45: 2297
        1.45 -     1.57: 10358
        1.57 -     1.69: 0
        1.69 -     1.81: 156
  Bond restraints: 19176
  Sorted by residual:
  bond pdb=" CB  THR E  91 "
       pdb=" CG2 THR E  91 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.15e-01
  bond pdb=" CB  THR D  91 "
       pdb=" CG2 THR D  91 "
    ideal  model  delta    sigma   weight residual
    1.521  1.492  0.029 3.30e-02 9.18e+02 7.96e-01
  bond pdb=" CB  THR F  91 "
       pdb=" CG2 THR F  91 "
    ideal  model  delta    sigma   weight residual
    1.521  1.492  0.029 3.30e-02 9.18e+02 7.89e-01
  bond pdb=" CB  THR B  91 "
       pdb=" CG2 THR B  91 "
    ideal  model  delta    sigma   weight residual
    1.521  1.492  0.029 3.30e-02 9.18e+02 7.84e-01
  bond pdb=" CB  THR C  91 "
       pdb=" CG2 THR C  91 "
    ideal  model  delta    sigma   weight residual
    1.521  1.492  0.029 3.30e-02 9.18e+02 7.78e-01
  ... (remaining 19171 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 25287
        1.62 -     3.23: 613
        3.23 -     4.85: 56
        4.85 -     6.46: 12
        6.46 -     8.08: 6
  Bond angle restraints: 25974
  Sorted by residual:
  angle pdb=" CA  GLY E 215 "
        pdb=" C   GLY E 215 "
        pdb=" O   GLY E 215 "
      ideal   model   delta    sigma   weight residual
     122.76  119.55    3.21 1.12e+00 7.97e-01 8.21e+00
  angle pdb=" CA  GLY A 215 "
        pdb=" C   GLY A 215 "
        pdb=" O   GLY A 215 "
      ideal   model   delta    sigma   weight residual
     122.76  119.57    3.19 1.12e+00 7.97e-01 8.12e+00
  angle pdb=" CA  GLY C 215 "
        pdb=" C   GLY C 215 "
        pdb=" O   GLY C 215 "
      ideal   model   delta    sigma   weight residual
     122.76  119.62    3.14 1.12e+00 7.97e-01 7.88e+00
  angle pdb=" CA  GLY D 215 "
        pdb=" C   GLY D 215 "
        pdb=" O   GLY D 215 "
      ideal   model   delta    sigma   weight residual
     122.76  119.64    3.12 1.12e+00 7.97e-01 7.76e+00
  angle pdb=" CA  GLY F 215 "
        pdb=" C   GLY F 215 "
        pdb=" O   GLY F 215 "
      ideal   model   delta    sigma   weight residual
     122.76  119.65    3.11 1.12e+00 7.97e-01 7.70e+00
  ... (remaining 25969 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 10116
       17.47 -    34.95: 1110
       34.95 -    52.42: 132
       52.42 -    69.90: 12
       69.90 -    87.37: 24
  Dihedral angle restraints: 11394
    sinusoidal: 4476
      harmonic: 6918
  Sorted by residual:
  dihedral pdb=" CA  PHE A 214 "
           pdb=" C   PHE A 214 "
           pdb=" N   GLY A 215 "
           pdb=" CA  GLY A 215 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.70   21.30     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" CA  PHE F 214 "
           pdb=" C   PHE F 214 "
           pdb=" N   GLY F 215 "
           pdb=" CA  GLY F 215 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.71   21.29     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" CA  PHE E 214 "
           pdb=" C   PHE E 214 "
           pdb=" N   GLY E 215 "
           pdb=" CA  GLY E 215 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.72   21.28     0      5.00e+00 4.00e-02 1.81e+01
  ... (remaining 11391 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1497
       0.026 -    0.053: 869
       0.053 -    0.079: 326
       0.079 -    0.105: 97
       0.105 -    0.132: 115
  Chirality restraints: 2904
  Sorted by residual:
  chirality pdb=" CA  ILE D  69 "
            pdb=" N   ILE D  69 "
            pdb=" C   ILE D  69 "
            pdb=" CB  ILE D  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.33e-01
  chirality pdb=" CA  ILE F  69 "
            pdb=" N   ILE F  69 "
            pdb=" C   ILE F  69 "
            pdb=" CB  ILE F  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.32e-01
  chirality pdb=" CA  ILE E  69 "
            pdb=" N   ILE E  69 "
            pdb=" C   ILE E  69 "
            pdb=" CB  ILE E  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.29e-01
  ... (remaining 2901 not shown)

  Planarity restraints: 3396
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E  11 "   -0.015 2.00e-02 2.50e+03   1.54e-02 4.16e+00
        pdb=" CG  PHE E  11 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 PHE E  11 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE E  11 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE E  11 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE E  11 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE E  11 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE F  11 "    0.015 2.00e-02 2.50e+03   1.53e-02 4.10e+00
        pdb=" CG  PHE F  11 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 PHE F  11 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE F  11 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE F  11 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE F  11 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE F  11 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D  11 "   -0.015 2.00e-02 2.50e+03   1.53e-02 4.09e+00
        pdb=" CG  PHE D  11 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 PHE D  11 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE D  11 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE D  11 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE D  11 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE D  11 "    0.002 2.00e-02 2.50e+03
  ... (remaining 3393 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 5742
        2.83 -     3.35: 17129
        3.35 -     3.86: 29900
        3.86 -     4.38: 33083
        4.38 -     4.90: 61723
  Nonbonded interactions: 147577
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS D 102 "
            pdb=" OD2 ASP D 142 "
     model   vdw
     2.309 3.120
  nonbonded pdb=" NZ  LYS F 102 "
            pdb=" OD2 ASP F 142 "
     model   vdw
     2.310 3.120
  nonbonded pdb=" NZ  LYS C 102 "
            pdb=" OD2 ASP C 142 "
     model   vdw
     2.310 3.120
  nonbonded pdb=" NZ  LYS E 102 "
            pdb=" OD2 ASP E 142 "
     model   vdw
     2.310 3.120
  nonbonded pdb=" NZ  LYS B 102 "
            pdb=" OD2 ASP B 142 "
     model   vdw
     2.310 3.120
  ... (remaining 147572 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'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.970
  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:             0.020
  Extract box with map and model:          0.660
  Check model and map are aligned:         0.140
  Set scattering table:                    0.170
  Process input model:                     40.850
  Find NCS groups from input model:        0.930
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.010
  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:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
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   0.030  19176  Z= 0.326
  Angle     :  0.590   8.077  25974  Z= 0.330
  Chirality :  0.043   0.132   2904
  Planarity :  0.004   0.045   3396
  Dihedral  : 14.021  87.372   6978
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.05 %
    Favored  : 99.95 %
  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:  0.78 (0.17), residues: 2448
  helix:  2.30 (0.14), residues: 1212
  sheet: -0.34 (0.27), residues: 426
  loop : -1.86 (0.17), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 348 
 HIS   0.003   0.001   HIS D 129 
 PHE   0.035   0.003   PHE E  11 
 TYR   0.008   0.001   TYR E  51 
 ARG   0.005   0.001   ARG C 402 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1974 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 250
  time to evaluate  : 2.088 
Fit side-chains
REVERT: A  303 LYS cc_start: 0.6542 (ptpt) cc_final: 0.5956 (pttt)
REVERT: B   87 MET cc_start: 0.8861 (tpp) cc_final: 0.8617 (tpp)
REVERT: B  303 LYS cc_start: 0.6756 (ptpt) cc_final: 0.6167 (pttt)
REVERT: C  303 LYS cc_start: 0.6873 (ptpt) cc_final: 0.6144 (pttt)
REVERT: D  150 MET cc_start: 0.8667 (mmp) cc_final: 0.8449 (mmt)
REVERT: D  238 ILE cc_start: 0.7859 (tp) cc_final: 0.7602 (mp)
REVERT: D  256 HIS cc_start: 0.7066 (t-170) cc_final: 0.6818 (t-170)
REVERT: E   65 MET cc_start: 0.8929 (mtt) cc_final: 0.8703 (mtt)
REVERT: E  212 GLN cc_start: 0.7639 (tt0) cc_final: 0.7296 (tt0)
REVERT: E  278 LEU cc_start: 0.7243 (mt) cc_final: 0.6940 (tt)
REVERT: F  212 GLN cc_start: 0.7762 (tt0) cc_final: 0.7497 (tt0)
REVERT: F  243 ARG cc_start: 0.6438 (ttt180) cc_final: 0.6198 (ttt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 250
  average time/residue: 0.3805
  time to fit residues: 136.3260
Evaluate side-chains
  171 residues out of total 1974 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 2.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 246
   random chunks:
   chunk 207 optimal weight:    1.9990
   chunk 186 optimal weight:    9.9990
   chunk 103 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 125 optimal weight:    4.9990
   chunk 99 optimal weight:    8.9990
   chunk 192 optimal weight:    0.1980
   chunk 74 optimal weight:    4.9990
   chunk 117 optimal weight:    0.7980
   chunk 143 optimal weight:    0.0670
   chunk 223 optimal weight:    1.9990
   overall best weight:    1.0122

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 405 GLN
B  85 GLN
C  85 GLN
D 212 GLN
** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.1510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  19176  Z= 0.165
  Angle     :  0.462   3.953  25974  Z= 0.251
  Chirality :  0.041   0.168   2904
  Planarity :  0.004   0.034   3396
  Dihedral  :  3.725  17.493   2616
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  6.43 %
    Favored  : 92.91 %
  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:  1.39 (0.17), residues: 2448
  helix:  2.65 (0.14), residues: 1230
  sheet:  0.28 (0.31), residues: 336
  loop : -1.44 (0.17), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 348 
 HIS   0.004   0.001   HIS D 280 
 PHE   0.027   0.001   PHE A  11 
 TYR   0.011   0.001   TYR A  51 
 ARG   0.005   0.000   ARG D 110 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1974 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 184
  time to evaluate  : 2.008 
Fit side-chains
REVERT: A  303 LYS cc_start: 0.6938 (ptpt) cc_final: 0.6297 (pttt)
REVERT: B  303 LYS cc_start: 0.6936 (ptpt) cc_final: 0.6061 (pttt)
REVERT: C   49 VAL cc_start: 0.8604 (t) cc_final: 0.8318 (p)
REVERT: C  281 GLU cc_start: 0.6385 (mm-30) cc_final: 0.6157 (mm-30)
REVERT: C  303 LYS cc_start: 0.7100 (ptpt) cc_final: 0.6044 (pttt)
REVERT: C  402 ARG cc_start: 0.7401 (ttp80) cc_final: 0.6915 (ttp80)
REVERT: E  283 ASP cc_start: 0.7393 (m-30) cc_final: 0.6263 (m-30)
REVERT: F  212 GLN cc_start: 0.7779 (tt0) cc_final: 0.7570 (tt0)
REVERT: F  238 ILE cc_start: 0.7651 (tp) cc_final: 0.7416 (mp)
  outliers start: 13
  outliers final: 9
  residues processed: 190
  average time/residue: 0.3575
  time to fit residues: 100.3637
Evaluate side-chains
  170 residues out of total 1974 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 161
  time to evaluate  : 2.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 MET
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain D residue  254 ILE
Chi-restraints excluded: chain E residue  254 ILE
Chi-restraints excluded: chain E residue  275 ASP
Chi-restraints excluded: chain E residue  379 THR
Chi-restraints excluded: chain F residue    7 THR
Chi-restraints excluded: chain F residue  379 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 246
   random chunks:
   chunk 124 optimal weight:    5.9990
   chunk 69 optimal weight:    4.9990
   chunk 185 optimal weight:    3.9990
   chunk 152 optimal weight:    9.9990
   chunk 61 optimal weight:    7.9990
   chunk 223 optimal weight:    6.9990
   chunk 241 optimal weight:    2.9990
   chunk 199 optimal weight:    5.9990
   chunk 221 optimal weight:    4.9990
   chunk 76 optimal weight:    0.8980
   chunk 179 optimal weight:    0.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 405 GLN
** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031  19176  Z= 0.305
  Angle     :  0.522   4.773  25974  Z= 0.283
  Chirality :  0.043   0.145   2904
  Planarity :  0.004   0.034   3396
  Dihedral  :  3.978  16.756   2616
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  9.12 %
    Favored  : 89.51 %
  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:  1.17 (0.17), residues: 2448
  helix:  2.54 (0.14), residues: 1230
  sheet: -0.20 (0.32), residues: 324
  loop : -1.46 (0.17), residues: 894

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D 348 
 HIS   0.004   0.001   HIS C 384 
 PHE   0.016   0.002   PHE C 374 
 TYR   0.012   0.001   TYR A  51 
 ARG   0.005   0.001   ARG D 110 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1974 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 177
  time to evaluate  : 2.152 
Fit side-chains
REVERT: A  303 LYS cc_start: 0.7134 (ptpt) cc_final: 0.6322 (pttt)
REVERT: B  281 GLU cc_start: 0.6420 (mm-30) cc_final: 0.6213 (mm-30)
REVERT: B  303 LYS cc_start: 0.7003 (ptpt) cc_final: 0.6077 (pttt)
REVERT: C  214 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7660 (m-10)
REVERT: C  303 LYS cc_start: 0.7125 (ptpt) cc_final: 0.5987 (pttt)
REVERT: C  381 CYS cc_start: 0.7836 (t) cc_final: 0.6978 (m)
REVERT: F  212 GLN cc_start: 0.7974 (tt0) cc_final: 0.7715 (tt0)
REVERT: F  278 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7464 (tt)
  outliers start: 27
  outliers final: 18
  residues processed: 192
  average time/residue: 0.3551
  time to fit residues: 101.2816
Evaluate side-chains
  187 residues out of total 1974 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 167
  time to evaluate  : 2.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 MET
Chi-restraints excluded: chain A residue  214 PHE
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain C residue  214 PHE
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  383 THR
Chi-restraints excluded: chain D residue  214 PHE
Chi-restraints excluded: chain E residue  214 PHE
Chi-restraints excluded: chain E residue  254 ILE
Chi-restraints excluded: chain E residue  258 ASP
Chi-restraints excluded: chain E residue  379 THR
Chi-restraints excluded: chain F residue  214 PHE
Chi-restraints excluded: chain F residue  242 ILE
Chi-restraints excluded: chain F residue  258 ASP
Chi-restraints excluded: chain F residue  278 LEU
Chi-restraints excluded: chain F residue  280 HIS
Chi-restraints excluded: chain F residue  290 LEU
Chi-restraints excluded: chain F residue  379 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 246
   random chunks:
   chunk 221 optimal weight:    7.9990
   chunk 168 optimal weight:    8.9990
   chunk 116 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 106 optimal weight:    8.9990
   chunk 150 optimal weight:    0.8980
   chunk 224 optimal weight:    3.9990
   chunk 237 optimal weight:    4.9990
   chunk 117 optimal weight:    0.8980
   chunk 212 optimal weight:    4.9990
   chunk 64 optimal weight:    9.9990
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 280 HIS
B 280 HIS
** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 384 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  19176  Z= 0.297
  Angle     :  0.505   4.623  25974  Z= 0.275
  Chirality :  0.043   0.141   2904
  Planarity :  0.004   0.033   3396
  Dihedral  :  3.952  15.654   2616
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 11.09 %
    Favored  : 87.13 %
  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:  1.13 (0.17), residues: 2448
  helix:  2.57 (0.14), residues: 1224
  sheet: -0.35 (0.31), residues: 330
  loop : -1.50 (0.17), residues: 894

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D 348 
 HIS   0.005   0.001   HIS A 384 
 PHE   0.015   0.002   PHE F 214 
 TYR   0.012   0.001   TYR A  51 
 ARG   0.006   0.001   ARG E 110 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1974 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 160
  time to evaluate  : 2.280 
Fit side-chains
REVERT: A  303 LYS cc_start: 0.7102 (ptpt) cc_final: 0.6336 (pttt)
REVERT: B  303 LYS cc_start: 0.7195 (ptpt) cc_final: 0.6370 (pttt)
REVERT: C  214 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7388 (m-10)
REVERT: C  281 GLU cc_start: 0.6406 (mm-30) cc_final: 0.6176 (mm-30)
REVERT: C  303 LYS cc_start: 0.7092 (ptpt) cc_final: 0.6061 (pttt)
REVERT: C  381 CYS cc_start: 0.7828 (t) cc_final: 0.6977 (m)
REVERT: E  143 MET cc_start: 0.7703 (ptm) cc_final: 0.7458 (ptm)
REVERT: F  212 GLN cc_start: 0.8078 (tt0) cc_final: 0.7791 (tt0)
REVERT: F  278 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7421 (tt)
  outliers start: 35
  outliers final: 20
  residues processed: 183
  average time/residue: 0.3648
  time to fit residues: 98.8620
Evaluate side-chains
  178 residues out of total 1974 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 156
  time to evaluate  : 2.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 MET
Chi-restraints excluded: chain A residue  214 PHE
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  383 THR
Chi-restraints excluded: chain C residue  143 MET
Chi-restraints excluded: chain C residue  214 PHE
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  383 THR
Chi-restraints excluded: chain D residue  214 PHE
Chi-restraints excluded: chain D residue  254 ILE
Chi-restraints excluded: chain E residue  214 PHE
Chi-restraints excluded: chain E residue  254 ILE
Chi-restraints excluded: chain E residue  258 ASP
Chi-restraints excluded: chain E residue  379 THR
Chi-restraints excluded: chain F residue  214 PHE
Chi-restraints excluded: chain F residue  242 ILE
Chi-restraints excluded: chain F residue  278 LEU
Chi-restraints excluded: chain F residue  280 HIS
Chi-restraints excluded: chain F residue  290 LEU
Chi-restraints excluded: chain F residue  379 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 246
   random chunks:
   chunk 198 optimal weight:    2.9990
   chunk 134 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 177 optimal weight:    3.9990
   chunk 98 optimal weight:    0.8980
   chunk 202 optimal weight:    4.9990
   chunk 164 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 121 optimal weight:    6.9990
   chunk 213 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Sorry: Reduce crashed with command 'molprobity.reduce  -quiet -trim -'.
Dumping stdin to file 'reduce_failure.pdb'.
Return code: -15
Dumping stderr: