Starting phenix.real_space_refine
on Fri Nov 15 20:56:14 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmy_29300/11_2024/8fmy_29300.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmy_29300/11_2024/8fmy_29300.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmy_29300/11_2024/8fmy_29300.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmy_29300/11_2024/8fmy_29300.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmy_29300/11_2024/8fmy_29300.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmy_29300/11_2024/8fmy_29300.cif"
  }
  resolution = 2.66
  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=   0.015
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      57      5.16       5
     C    6036      2.51       5
     N    1611      2.21       5
     O    1893      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 9597
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3199
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 3199
          Classifications: {'peptide': 420}
          Link IDs: {'PTRANS': 13, 'TRANS': 406}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 5.86, per 1000 atoms: 0.61
  Number of scatterers: 9597
  At special positions: 0
  Unit cell: (103, 104, 98, 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      57     16.00
     O    1893      8.00
     N    1611      7.00
     C    6036      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 330 " - pdb=" SG  CYS A 339 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 354 " - pdb=" SG  CYS A 362 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 386 " - pdb=" SG  CYS A 391 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 393 " - pdb=" SG  CYS A 416 " distance=2.04

  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: 2.34
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2358

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 15 sheets defined
      40.0% alpha, 22.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 33
      removed outlier: 3.556A  pdb=" N   LEU A  32 " --> pdb=" O   HIS A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 70
    Processing helix  chain 'A' and resid 71 through 105
      removed outlier: 3.500A  pdb=" N   GLU A  77 " --> pdb=" O   LYS A  73 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ASN A  80 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU A  81 " --> pdb=" O   GLU A  77 " (cutoff:3.500A)
      Proline residue:  A  88  - end of helix
      removed outlier: 3.930A  pdb=" N   MET A  91 " --> pdb=" O   GLU A  87 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ALA A  92 " --> pdb=" O   PRO A  88 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASN A  99 " --> pdb=" O   THR A  95 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   VAL A 100 " --> pdb=" O   MET A  96 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   GLY A 103 " --> pdb=" O   ASN A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 120
    Processing helix  chain 'A' and resid 124 through 136
      removed outlier: 3.650A  pdb=" N   HIS A 134 " --> pdb=" O   GLY A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 145
      removed outlier: 3.619A  pdb=" N   ALA A 140 " --> pdb=" O   SER A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 152
    Processing helix  chain 'A' and resid 172 through 182
      removed outlier: 3.628A  pdb=" N   GLY A 176 " --> pdb=" O   ASP A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 186
      removed outlier: 3.565A  pdb=" N   ILE A 186 " --> pdb=" O   ILE A 183 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 183 through 186'
    Processing helix  chain 'A' and resid 190 through 219
      removed outlier: 3.668A  pdb=" N   ILE A 200 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ARG A 201 " --> pdb=" O   SER A 197 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR A 203 " --> pdb=" O   GLY A 199 " (cutoff:3.500A)
      Proline residue:  A 215  - end of helix
      removed outlier: 3.521A  pdb=" N   GLN A 218 " --> pdb=" O   GLY A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 231
    Processing helix  chain 'A' and resid 232 through 235
      removed outlier: 4.100A  pdb=" N   ASN A 235 " --> pdb=" O   SER A 232 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 232 through 235'
    Processing helix  chain 'A' and resid 237 through 245
      removed outlier: 3.763A  pdb=" N   LEU A 241 " --> pdb=" O   ASN A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 258
      removed outlier: 3.619A  pdb=" N   SER A 258 " --> pdb=" O   GLU A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 330
    Processing helix  chain 'A' and resid 348 through 356
    Processing helix  chain 'A' and resid 358 through 362
    Processing helix  chain 'B' and resid 28 through 33
      removed outlier: 3.557A  pdb=" N   LEU B  32 " --> pdb=" O   HIS B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 70
    Processing helix  chain 'B' and resid 71 through 105
      removed outlier: 3.751A  pdb=" N   ASN B  80 " --> pdb=" O   ASP B  76 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU B  81 " --> pdb=" O   GLU B  77 " (cutoff:3.500A)
      Proline residue:  B  88  - end of helix
      removed outlier: 3.930A  pdb=" N   MET B  91 " --> pdb=" O   GLU B  87 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ALA B  92 " --> pdb=" O   PRO B  88 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASN B  99 " --> pdb=" O   THR B  95 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   VAL B 100 " --> pdb=" O   MET B  96 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   GLY B 103 " --> pdb=" O   ASN B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 120
    Processing helix  chain 'B' and resid 124 through 136
      removed outlier: 3.650A  pdb=" N   HIS B 134 " --> pdb=" O   GLY B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 145
      removed outlier: 3.619A  pdb=" N   ALA B 140 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 152
    Processing helix  chain 'B' and resid 172 through 182
      removed outlier: 3.628A  pdb=" N   GLY B 176 " --> pdb=" O   ASP B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 186
      removed outlier: 3.565A  pdb=" N   ILE B 186 " --> pdb=" O   ILE B 183 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 183 through 186'
    Processing helix  chain 'B' and resid 190 through 219
      removed outlier: 3.667A  pdb=" N   ILE B 200 " --> pdb=" O   LEU B 196 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ARG B 201 " --> pdb=" O   SER B 197 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR B 203 " --> pdb=" O   GLY B 199 " (cutoff:3.500A)
      Proline residue:  B 215  - end of helix
      removed outlier: 3.521A  pdb=" N   GLN B 218 " --> pdb=" O   GLY B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 231
    Processing helix  chain 'B' and resid 232 through 235
      removed outlier: 4.101A  pdb=" N   ASN B 235 " --> pdb=" O   SER B 232 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 232 through 235'
    Processing helix  chain 'B' and resid 237 through 245
      removed outlier: 3.762A  pdb=" N   LEU B 241 " --> pdb=" O   ASN B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 258
      removed outlier: 3.620A  pdb=" N   SER B 258 " --> pdb=" O   GLU B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 330
    Processing helix  chain 'B' and resid 348 through 356
    Processing helix  chain 'B' and resid 358 through 362
    Processing helix  chain 'C' and resid 28 through 33
      removed outlier: 3.557A  pdb=" N   LEU C  32 " --> pdb=" O   HIS C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 70
    Processing helix  chain 'C' and resid 71 through 105
      removed outlier: 3.750A  pdb=" N   ASN C  80 " --> pdb=" O   ASP C  76 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU C  81 " --> pdb=" O   GLU C  77 " (cutoff:3.500A)
      Proline residue:  C  88  - end of helix
      removed outlier: 3.931A  pdb=" N   MET C  91 " --> pdb=" O   GLU C  87 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ALA C  92 " --> pdb=" O   PRO C  88 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASN C  99 " --> pdb=" O   THR C  95 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   VAL C 100 " --> pdb=" O   MET C  96 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   GLY C 103 " --> pdb=" O   ASN C  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 116 through 120
    Processing helix  chain 'C' and resid 124 through 136
      removed outlier: 3.651A  pdb=" N   HIS C 134 " --> pdb=" O   GLY C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 136 through 145
      removed outlier: 3.618A  pdb=" N   ALA C 140 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 146 through 152
    Processing helix  chain 'C' and resid 172 through 182
      removed outlier: 3.628A  pdb=" N   GLY C 176 " --> pdb=" O   ASP C 172 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 186
      removed outlier: 3.565A  pdb=" N   ILE C 186 " --> pdb=" O   ILE C 183 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 183 through 186'
    Processing helix  chain 'C' and resid 190 through 219
      removed outlier: 3.667A  pdb=" N   ILE C 200 " --> pdb=" O   LEU C 196 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ARG C 201 " --> pdb=" O   SER C 197 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   THR C 203 " --> pdb=" O   GLY C 199 " (cutoff:3.500A)
      Proline residue:  C 215  - end of helix
      removed outlier: 3.521A  pdb=" N   GLN C 218 " --> pdb=" O   GLY C 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 227 through 231
    Processing helix  chain 'C' and resid 232 through 235
      removed outlier: 4.100A  pdb=" N   ASN C 235 " --> pdb=" O   SER C 232 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 232 through 235'
    Processing helix  chain 'C' and resid 237 through 245
      removed outlier: 3.762A  pdb=" N   LEU C 241 " --> pdb=" O   ASN C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 252 through 258
      removed outlier: 3.619A  pdb=" N   SER C 258 " --> pdb=" O   GLU C 254 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 327 through 330
    Processing helix  chain 'C' and resid 348 through 356
    Processing helix  chain 'C' and resid 358 through 362
    Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 332
      removed outlier: 3.643A  pdb=" N   LYS A  48 " --> pdb=" O   CYS A 339 " (cutoff:3.500A)
      removed outlier: 5.226A  pdb=" N   GLU A 294 " --> pdb=" O   GLY A  40 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   THR A  42 " --> pdb=" O   VAL A 292 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   VAL A 292 " --> pdb=" O   THR A  42 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   ASN A  44 " --> pdb=" O   ALA A 290 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   ALA A 290 " --> pdb=" O   ASN A  44 " (cutoff:3.500A)
      removed outlier: 9.704A  pdb=" N   LYS A  46 " --> pdb=" O   PRO A 288 " (cutoff:3.500A)
      removed outlier: 9.493A  pdb=" N   LYS A  48 " --> pdb=" O   LEU A 286 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   LEU A 286 " --> pdb=" O   LYS A  48 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   PHE A 314 " --> pdb=" O   ILE A 325 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   ILE A 325 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 161
      removed outlier: 8.404A  pdb=" N   THR A 167 " --> pdb=" O   THR A  53 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   LEU A  55 " --> pdb=" O   THR A 167 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ASP A 267 " --> pdb=" O   ALA A 276 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   GLU A 278 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 5.792A  pdb=" N   ILE A 265 " --> pdb=" O   GLU A 278 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   GLU A 280 " --> pdb=" O   GLY A 263 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   GLY A 263 " --> pdb=" O   GLU A 280 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 115
    Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 123
    Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 302
    Processing sheet with id=AA6, first strand: chain 'A' and resid 409 through 411
    Processing sheet with id=AA7, first strand: chain 'A' and resid 398 through 399
      removed outlier: 7.065A  pdb=" N   LEU A 425 " --> pdb=" O   MET B 114 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 331 through 332
      removed outlier: 3.643A  pdb=" N   LYS B  48 " --> pdb=" O   CYS B 339 " (cutoff:3.500A)
      removed outlier: 5.226A  pdb=" N   GLU B 294 " --> pdb=" O   GLY B  40 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   THR B  42 " --> pdb=" O   VAL B 292 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   VAL B 292 " --> pdb=" O   THR B  42 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   ASN B  44 " --> pdb=" O   ALA B 290 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   ALA B 290 " --> pdb=" O   ASN B  44 " (cutoff:3.500A)
      removed outlier: 9.705A  pdb=" N   LYS B  46 " --> pdb=" O   PRO B 288 " (cutoff:3.500A)
      removed outlier: 9.494A  pdb=" N   LYS B  48 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.984A  pdb=" N   LEU B 286 " --> pdb=" O   LYS B  48 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   PHE B 314 " --> pdb=" O   ILE B 325 " (cutoff:3.500A)
      removed outlier: 4.756A  pdb=" N   ILE B 325 " --> pdb=" O   PHE B 314 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 157 through 161
      removed outlier: 8.403A  pdb=" N   THR B 167 " --> pdb=" O   THR B  53 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   LEU B  55 " --> pdb=" O   THR B 167 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ASP B 267 " --> pdb=" O   ALA B 276 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   GLU B 278 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   ILE B 265 " --> pdb=" O   GLU B 278 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   GLU B 280 " --> pdb=" O   GLY B 263 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   GLY B 263 " --> pdb=" O   GLU B 280 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 300 through 302
    Processing sheet with id=AB2, first strand: chain 'B' and resid 409 through 411
    Processing sheet with id=AB3, first strand: chain 'B' and resid 398 through 399
      removed outlier: 7.080A  pdb=" N   LEU B 425 " --> pdb=" O   MET C 114 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 331 through 332
      removed outlier: 3.642A  pdb=" N   LYS C  48 " --> pdb=" O   CYS C 339 " (cutoff:3.500A)
      removed outlier: 5.226A  pdb=" N   GLU C 294 " --> pdb=" O   GLY C  40 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   THR C  42 " --> pdb=" O   VAL C 292 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   VAL C 292 " --> pdb=" O   THR C  42 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   ASN C  44 " --> pdb=" O   ALA C 290 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   ALA C 290 " --> pdb=" O   ASN C  44 " (cutoff:3.500A)
      removed outlier: 9.704A  pdb=" N   LYS C  46 " --> pdb=" O   PRO C 288 " (cutoff:3.500A)
      removed outlier: 9.494A  pdb=" N   LYS C  48 " --> pdb=" O   LEU C 286 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   LEU C 286 " --> pdb=" O   LYS C  48 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   PHE C 314 " --> pdb=" O   ILE C 325 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   ILE C 325 " --> pdb=" O   PHE C 314 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 161
      removed outlier: 8.403A  pdb=" N   THR C 167 " --> pdb=" O   THR C  53 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   LEU C  55 " --> pdb=" O   THR C 167 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ASP C 267 " --> pdb=" O   ALA C 276 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   GLU C 278 " --> pdb=" O   ILE C 265 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   ILE C 265 " --> pdb=" O   GLU C 278 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   GLU C 280 " --> pdb=" O   GLY C 263 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   GLY C 263 " --> pdb=" O   GLU C 280 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 300 through 302

    424 hydrogen bonds defined for protein.
    1146 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: 3.27

  Time building geometry restraints manager: 2.72 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2997
        1.34 -     1.46: 1888
        1.46 -     1.59: 4757
        1.59 -     1.72: 0
        1.72 -     1.84: 84
  Bond restraints: 9726
  Sorted by residual:
  bond pdb=" N   ASP C 172 "
       pdb=" CA  ASP C 172 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.037 2.20e-02 2.07e+03 2.76e+00
  bond pdb=" N   ASP A 172 "
       pdb=" CA  ASP A 172 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.036 2.20e-02 2.07e+03 2.75e+00
  bond pdb=" N   ASP B 172 "
       pdb=" CA  ASP B 172 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.036 2.20e-02 2.07e+03 2.67e+00
  bond pdb=" CA  THR B 173 "
       pdb=" C   THR B 173 "
    ideal  model  delta    sigma   weight residual
    1.524  1.542 -0.019 1.27e-02 6.20e+03 2.12e+00
  bond pdb=" CA  THR C 173 "
       pdb=" C   THR C 173 "
    ideal  model  delta    sigma   weight residual
    1.524  1.542 -0.018 1.27e-02 6.20e+03 2.02e+00
  ... (remaining 9721 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 11284
        1.48 -     2.96: 1502
        2.96 -     4.43: 339
        4.43 -     5.91: 76
        5.91 -     7.39: 23
  Bond angle restraints: 13224
  Sorted by residual:
  angle pdb=" N   THR B 173 "
        pdb=" CA  THR B 173 "
        pdb=" C   THR B 173 "
      ideal   model   delta    sigma   weight residual
     111.07  115.94   -4.87 1.07e+00 8.73e-01 2.07e+01
  angle pdb=" N   THR C 173 "
        pdb=" CA  THR C 173 "
        pdb=" C   THR C 173 "
      ideal   model   delta    sigma   weight residual
     111.07  115.93   -4.86 1.07e+00 8.73e-01 2.06e+01
  angle pdb=" N   THR A 173 "
        pdb=" CA  THR A 173 "
        pdb=" C   THR A 173 "
      ideal   model   delta    sigma   weight residual
     111.07  115.89   -4.82 1.07e+00 8.73e-01 2.03e+01
  angle pdb=" N   LYS B  68 "
        pdb=" CA  LYS B  68 "
        pdb=" C   LYS B  68 "
      ideal   model   delta    sigma   weight residual
     111.33  116.31   -4.98 1.21e+00 6.83e-01 1.70e+01
  angle pdb=" N   LYS C  68 "
        pdb=" CA  LYS C  68 "
        pdb=" C   LYS C  68 "
      ideal   model   delta    sigma   weight residual
     111.33  116.29   -4.96 1.21e+00 6.83e-01 1.68e+01
  ... (remaining 13219 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.33: 5494
       15.33 -    30.65: 342
       30.65 -    45.98: 62
       45.98 -    61.31: 27
       61.31 -    76.64: 18
  Dihedral angle restraints: 5943
    sinusoidal: 2274
      harmonic: 3669
  Sorted by residual:
  dihedral pdb=" CB  CYS A 393 "
           pdb=" SG  CYS A 393 "
           pdb=" SG  CYS A 416 "
           pdb=" CB  CYS A 416 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.08  -60.08     1      1.00e+01 1.00e-02 4.81e+01
  dihedral pdb=" CA  ASP A 440 "
           pdb=" C   ASP A 440 "
           pdb=" N   ASN A 441 "
           pdb=" CA  ASN A 441 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.23   16.77     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CA  ASP B 440 "
           pdb=" C   ASP B 440 "
           pdb=" N   ASN B 441 "
           pdb=" CA  ASN B 441 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.24   16.76     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 5940 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 782
       0.039 -    0.077: 496
       0.077 -    0.116: 233
       0.116 -    0.155: 85
       0.155 -    0.193: 18
  Chirality restraints: 1614
  Sorted by residual:
  chirality pdb=" CA  ILE C 183 "
            pdb=" N   ILE C 183 "
            pdb=" C   ILE C 183 "
            pdb=" CB  ILE C 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.24    0.19 2.00e-01 2.50e+01 9.33e-01
  chirality pdb=" CA  ILE A 183 "
            pdb=" N   ILE A 183 "
            pdb=" C   ILE A 183 "
            pdb=" CB  ILE A 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.24    0.19 2.00e-01 2.50e+01 9.11e-01
  chirality pdb=" CA  ILE B 183 "
            pdb=" N   ILE B 183 "
            pdb=" C   ILE B 183 "
            pdb=" CB  ILE B 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.24    0.19 2.00e-01 2.50e+01 9.00e-01
  ... (remaining 1611 not shown)

  Planarity restraints: 1695
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 210 "   -0.017 2.00e-02 2.50e+03   3.44e-02 1.19e+01
        pdb=" C   ILE A 210 "    0.060 2.00e-02 2.50e+03
        pdb=" O   ILE A 210 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   THR A 211 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 210 "   -0.017 2.00e-02 2.50e+03   3.43e-02 1.17e+01
        pdb=" C   ILE B 210 "    0.059 2.00e-02 2.50e+03
        pdb=" O   ILE B 210 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   THR B 211 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C 210 "    0.017 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        pdb=" C   ILE C 210 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   ILE C 210 "    0.022 2.00e-02 2.50e+03
        pdb=" N   THR C 211 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1692 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 20
        2.61 -     3.18: 7854
        3.18 -     3.75: 12638
        3.75 -     4.33: 18293
        4.33 -     4.90: 31002
  Nonbonded interactions: 69807
  Sorted by model distance:
  nonbonded pdb=" SG  CYS C 330 "
            pdb=" SG  CYS C 339 "
     model   vdw
     2.034 3.760
  nonbonded pdb=" SG  CYS B 330 "
            pdb=" SG  CYS B 339 "
     model   vdw
     2.035 3.760
  nonbonded pdb=" SG  CYS B 393 "
            pdb=" SG  CYS B 416 "
     model   vdw
     2.040 3.760
  nonbonded pdb=" SG  CYS C 393 "
            pdb=" SG  CYS C 416 "
     model   vdw
     2.040 3.760
  nonbonded pdb=" SG  CYS B 354 "
            pdb=" SG  CYS B 362 "
     model   vdw
     2.041 3.760
  ... (remaining 69802 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'
}

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:             0.670
  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:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.280
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:15.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
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      :  0.008   0.050   9726  Z= 0.545
  Angle     :  1.159   7.388  13224  Z= 0.715
  Chirality :  0.062   0.193   1614
  Planarity :  0.007   0.049   1695
  Dihedral  : 12.096  76.635   3573
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 0.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  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: -1.16 (0.21), residues: 1254
  helix: -1.03 (0.21), residues: 402
  sheet:  0.31 (0.31), residues: 258
  loop : -0.98 (0.23), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.007   TRP B 307 
 HIS   0.006   0.002   HIS B 257 
 PHE   0.023   0.005   PHE C 281 
 TYR   0.042   0.006   TYR A  45 
 ARG   0.013   0.002   ARG A 364 

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 1.270 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 1.7978
  time to fit residues: 108.6625
Evaluate side-chains
  32 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 98 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 114 optimal weight:    3.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
B 349 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9726  Z= 0.267
  Angle     :  0.639   5.625  13224  Z= 0.365
  Chirality :  0.046   0.140   1614
  Planarity :  0.004   0.051   1695
  Dihedral  :  5.080  18.435   1350
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  4.13 %
    Favored  : 95.04 %
  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 (0.23), residues: 1254
  helix:  1.03 (0.25), residues: 405
  sheet:  0.54 (0.32), residues: 252
  loop : -0.52 (0.25), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.003   TRP C 307 
 HIS   0.003   0.001   HIS B 257 
 PHE   0.012   0.002   PHE A 234 
 TYR   0.014   0.002   TYR A  45 
 ARG   0.003   0.000   ARG A 108 

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 34
  time to evaluate  : 1.224 
Fit side-chains
REVERT: A  296 MET cc_start: 0.8828 (mtm) cc_final: 0.8590 (mtp)
REVERT: B  349 HIS cc_start: 0.7070 (OUTLIER) cc_final: 0.6780 (t-90)
REVERT: B  426 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8600 (tt)
  outliers start: 9
  outliers final: 2
  residues processed: 39
  average time/residue: 1.2547
  time to fit residues: 53.6465
Evaluate side-chains
  31 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 27
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain B residue  349 HIS
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain C residue  349 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 114 optimal weight:    5.9990
   chunk 123 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 91 optimal weight:    5.9990
   overall best weight:    1.9786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8594
moved from start:          0.1972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9726  Z= 0.282
  Angle     :  0.591   6.254  13224  Z= 0.335
  Chirality :  0.045   0.145   1614
  Planarity :  0.004   0.034   1695
  Dihedral  :  4.876  16.841   1350
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 1.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  5.14 %
    Favored  : 93.94 %
  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:  0.64 (0.24), residues: 1254
  helix:  1.98 (0.27), residues: 369
  sheet:  0.30 (0.32), residues: 246
  loop : -0.42 (0.25), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 307 
 HIS   0.012   0.001   HIS B 349 
 PHE   0.012   0.002   PHE B 238 
 TYR   0.013   0.002   TYR A 274 
 ARG   0.002   0.000   ARG A 201 

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 27
  time to evaluate  : 1.222 
Fit side-chains
REVERT: B  349 HIS cc_start: 0.6943 (OUTLIER) cc_final: 0.6642 (t70)
REVERT: B  426 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8642 (tt)
  outliers start: 10
  outliers final: 3
  residues processed: 34
  average time/residue: 1.3770
  time to fit residues: 51.4995
Evaluate side-chains
  32 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 27
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain B residue  349 HIS
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain C residue  349 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 113 optimal weight:    3.9990
   chunk 86 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 115 optimal weight:    1.9990
   chunk 121 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
B 301 ASN
B 349 HIS
C 301 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.2295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9726  Z= 0.193
  Angle     :  0.516   5.237  13224  Z= 0.292
  Chirality :  0.044   0.139   1614
  Planarity :  0.003   0.038   1695
  Dihedral  :  4.584  16.261   1350
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 1.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  6.70 %
    Favored  : 92.65 %
  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:  0.62 (0.24), residues: 1254
  helix:  2.11 (0.27), residues: 375
  sheet:  0.22 (0.31), residues: 255
  loop : -0.54 (0.25), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 307 
 HIS   0.003   0.001   HIS B 349 
 PHE   0.008   0.002   PHE A 234 
 TYR   0.011   0.001   TYR A 274 
 ARG   0.002   0.000   ARG A 108 

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 1.248 
Fit side-chains
REVERT: B  349 HIS cc_start: 0.7063 (OUTLIER) cc_final: 0.6793 (t-90)
REVERT: B  426 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8646 (tt)
  outliers start: 7
  outliers final: 1
  residues processed: 35
  average time/residue: 1.4426
  time to fit residues: 55.5032
Evaluate side-chains
  30 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 1.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain B residue  349 HIS
Chi-restraints excluded: chain B residue  426 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 1 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 103 optimal weight:    0.0470
   chunk 84 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    1.3484

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

Flipped N/Q/H residues before XYZ refinement:
A 301 ASN
B 349 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9726  Z= 0.200
  Angle     :  0.506   4.984  13224  Z= 0.286
  Chirality :  0.043   0.133   1614
  Planarity :  0.003   0.034   1695
  Dihedral  :  4.477  16.151   1350
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 1.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  7.16 %
    Favored  : 91.74 %
  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:  0.65 (0.24), residues: 1254
  helix:  2.24 (0.27), residues: 375
  sheet:  0.17 (0.31), residues: 255
  loop : -0.57 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 307 
 HIS   0.002   0.001   HIS C 134 
 PHE   0.009   0.002   PHE B 238 
 TYR   0.012   0.001   TYR A 274 
 ARG   0.002   0.000   ARG A 108 

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 27
  time to evaluate  : 1.128 
Fit side-chains
REVERT: B  426 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8644 (tt)
  outliers start: 12
  outliers final: 7
  residues processed: 39
  average time/residue: 1.2058
  time to fit residues: 51.7364
Evaluate side-chains
  35 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 27
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  349 HIS
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  349 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 109 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 30 optimal weight:    5.9990
   chunk 121 optimal weight:    1.9990
   chunk 101 optimal weight:    5.9990
   chunk 56 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 117 optimal weight:    0.9990
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
B 349 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9726  Z= 0.216
  Angle     :  0.507   4.512  13224  Z= 0.287
  Chirality :  0.043   0.134   1614
  Planarity :  0.003   0.036   1695
  Dihedral  :  4.442  16.097   1350
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 1.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  7.71 %
    Favored  : 91.28 %
  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:  0.64 (0.24), residues: 1254
  helix:  2.26 (0.27), residues: 375
  sheet:  0.14 (0.31), residues: 255
  loop : -0.59 (0.25), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 307 
 HIS   0.004   0.001   HIS B 349 
 PHE   0.010   0.002   PHE B 238 
 TYR   0.012   0.001   TYR A 274 
 ARG   0.001   0.000   ARG C 108 

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 28
  time to evaluate  : 1.135 
Fit side-chains
REVERT: B  426 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8649 (tt)
  outliers start: 11
  outliers final: 7
  residues processed: 39
  average time/residue: 1.2559
  time to fit residues: 53.9186
Evaluate side-chains
  35 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 27
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  393 CYS
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  349 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 13 optimal weight:    0.0870
   chunk 69 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 102 optimal weight:    1.9990
   chunk 121 optimal weight:    3.9990
   chunk 76 optimal weight:    0.0020
   chunk 74 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.5166

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

Flipped N/Q/H residues before XYZ refinement:
B 349 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9726  Z= 0.111
  Angle     :  0.441   4.869  13224  Z= 0.248
  Chirality :  0.042   0.125   1614
  Planarity :  0.003   0.032   1695
  Dihedral  :  4.175  16.218   1350
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 1.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  8.26 %
    Favored  : 90.91 %
  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:  0.86 (0.24), residues: 1254
  helix:  2.37 (0.27), residues: 375
  sheet:  0.44 (0.32), residues: 258
  loop : -0.48 (0.25), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP C 307 
 HIS   0.002   0.001   HIS B 349 
 PHE   0.005   0.001   PHE B 375 
 TYR   0.008   0.001   TYR C 274 
 ARG   0.002   0.000   ARG C 415 

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 29
  time to evaluate  : 1.011 
Fit side-chains
REVERT: B  426 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8567 (tt)
  outliers start: 9
  outliers final: 3
  residues processed: 37
  average time/residue: 1.2827
  time to fit residues: 52.0586
Evaluate side-chains
  32 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  393 CYS
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain C residue  349 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 77 optimal weight:    0.5980
   chunk 82 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9980
   chunk 110 optimal weight:    6.9990
   chunk 116 optimal weight:    4.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.3184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.2704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9726  Z= 0.190
  Angle     :  0.500  11.077  13224  Z= 0.275
  Chirality :  0.043   0.132   1614
  Planarity :  0.003   0.035   1695
  Dihedral  :  4.207  16.136   1350
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 1.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  8.17 %
    Favored  : 91.18 %
  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:  0.91 (0.24), residues: 1254
  helix:  2.42 (0.28), residues: 375
  sheet:  0.37 (0.30), residues: 288
  loop : -0.46 (0.26), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 307 
 HIS   0.003   0.001   HIS B 349 
 PHE   0.010   0.002   PHE B 238 
 TYR   0.012   0.001   TYR A 274 
 ARG   0.001   0.000   ARG C 415 

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 1.075 
Fit side-chains
REVERT: B  426 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8634 (tt)
  outliers start: 7
  outliers final: 4
  residues processed: 34
  average time/residue: 1.3102
  time to fit residues: 48.8914
Evaluate side-chains
  32 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 27
  time to evaluate  : 1.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  393 CYS
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain C residue  349 HIS
Chi-restraints excluded: chain C residue  404 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 113 optimal weight:    4.9990
   chunk 116 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 88 optimal weight:    7.9990
   chunk 34 optimal weight:    4.9990
   chunk 102 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 112 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 119 optimal weight:    2.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 324 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9726  Z= 0.273
  Angle     :  0.545  11.314  13224  Z= 0.301
  Chirality :  0.044   0.137   1614
  Planarity :  0.003   0.035   1695
  Dihedral  :  4.421  16.719   1350
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 1.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  8.08 %
    Favored  : 90.91 %
  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:  0.68 (0.24), residues: 1254
  helix:  2.36 (0.28), residues: 375
  sheet:  0.12 (0.32), residues: 255
  loop : -0.58 (0.25), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 307 
 HIS   0.003   0.001   HIS C 134 
 PHE   0.012   0.002   PHE B 238 
 TYR   0.014   0.001   TYR A 274 
 ARG   0.001   0.000   ARG C 108 

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 28
  time to evaluate  : 1.158 
Fit side-chains
REVERT: A  146 MET cc_start: 0.8092 (mmm) cc_final: 0.7780 (mtp)
REVERT: B  426 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8675 (tt)
  outliers start: 11
  outliers final: 7
  residues processed: 39
  average time/residue: 1.2101
  time to fit residues: 51.9958
Evaluate side-chains
  36 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 28
  time to evaluate  : 1.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  225 ILE
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  393 CYS
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  349 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 83 optimal weight:   10.0000
   chunk 125 optimal weight:    8.9990
   chunk 115 optimal weight:    6.9990
   chunk 99 optimal weight:    0.0040
   chunk 10 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 79 optimal weight:    0.0670
   chunk 106 optimal weight:    0.0010
   overall best weight:    0.3936

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.3008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9726  Z= 0.108
  Angle     :  0.458  11.388  13224  Z= 0.246
  Chirality :  0.042   0.129   1614
  Planarity :  0.003   0.031   1695
  Dihedral  :  4.057  16.001   1350
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 1.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  8.91 %
    Favored  : 90.63 %
  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:  0.94 (0.24), residues: 1254
  helix:  2.52 (0.28), residues: 372
  sheet:  0.47 (0.33), residues: 258
  loop : -0.48 (0.25), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP C 307 
 HIS   0.003   0.001   HIS B 349 
 PHE   0.006   0.001   PHE B 375 
 TYR   0.008   0.001   TYR A 274 
 ARG   0.001   0.000   ARG C 415 

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 1.076 
Fit side-chains
REVERT: A  146 MET cc_start: 0.7920 (mmm) cc_final: 0.7621 (mtp)
REVERT: B  426 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8572 (tt)
  outliers start: 5
  outliers final: 3
  residues processed: 36
  average time/residue: 1.2759
  time to fit residues: 50.4016
Evaluate side-chains
  33 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  393 CYS
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain C residue  349 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 92 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 102 optimal weight:    0.8980
   chunk 12 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 87 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    1.1586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.069713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.056218 restraints weight = 22169.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.2860 rms_B_bonded: 3.47
r_work: 0.2715 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9726  Z= 0.177
  Angle     :  0.506  11.618  13224  Z= 0.270
  Chirality :  0.042   0.128   1614
  Planarity :  0.003   0.035   1695
  Dihedral  :  4.086  16.377   1350
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 1.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  8.82 %
    Favored  : 90.54 %
  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:  0.97 (0.24), residues: 1254
  helix:  2.53 (0.28), residues: 375
  sheet:  0.37 (0.30), residues: 288
  loop : -0.44 (0.26), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 307 
 HIS   0.002   0.001   HIS B 349 
 PHE   0.009   0.001   PHE B 238 
 TYR   0.011   0.001   TYR A 274 
 ARG   0.001   0.000   ARG C 415 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2170.54 seconds
wall clock time: 40 minutes 33.54 seconds (2433.54 seconds total)