Starting phenix.real_space_refine
on Thu Nov 14 17:13:07 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8j_36071/11_2024/8j8j_36071.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8j_36071/11_2024/8j8j_36071.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8j_36071/11_2024/8j8j_36071.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8j_36071/11_2024/8j8j_36071.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8j_36071/11_2024/8j8j_36071.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8j_36071/11_2024/8j8j_36071.cif"
  }
  resolution = 2.76
  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=   0.002 sd=   0.101
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: 6
    Type Number    sf(0)   Gaussians
     P      12      5.49       5
     Mg      3      5.21       5
     S      30      5.16       5
     C    4515      2.51       5
     N    1104      2.21       5
     O    1209      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 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: 6873
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "D"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2217
          Classifications: {'peptide': 290}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 280}
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2217
          Classifications: {'peptide': 290}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 280}
    Chain: "B"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2217
          Classifications: {'peptide': 290}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 280}
    Chain: "D"
      Number of atoms: 74
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 74
          Unusual residues: {' MG': 1, 'PGW': 1, 'PRP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 74
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 74
          Unusual residues: {' MG': 1, 'PGW': 1, 'PRP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 74
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 74
          Unusual residues: {' MG': 1, 'PGW': 1, 'PRP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 4.81, per 1000 atoms: 0.70
  Number of scatterers: 6873
  At special positions: 0
  Unit cell: (107.52, 99.84, 73.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      30     16.00
     P      12     15.00
     Mg      3     11.99
     O    1209      8.00
     N    1104      7.00
     C    4515      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.97
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1614

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 0 sheets defined
      82.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'D' and resid 13 through 18
      removed outlier: 3.667A  pdb=" N   VAL D  18 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 22 through 32
      removed outlier: 4.018A  pdb=" N   VAL D  27 " --> pdb=" O   ARG D  24 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LYS D  28 " --> pdb=" O   GLN D  25 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL D  30 " --> pdb=" O   VAL D  27 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU D  31 " --> pdb=" O   LYS D  28 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   VAL D  32 " --> pdb=" O   ASN D  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 33 through 39
      removed outlier: 3.768A  pdb=" N   LEU D  37 " --> pdb=" O   LEU D  33 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 49 through 77
      removed outlier: 3.888A  pdb=" N   SER D  56 " --> pdb=" O   LEU D  52 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   MET D  57 " --> pdb=" O   SER D  53 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   VAL D  60 " --> pdb=" O   SER D  56 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ALA D  65 " --> pdb=" O   VAL D  61 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   VAL D  75 " --> pdb=" O   LEU D  71 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ASP D  77 " --> pdb=" O   ASN D  73 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 121
    Processing helix  chain 'D' and resid 123 through 139
      removed outlier: 3.575A  pdb=" N   VAL D 127 " --> pdb=" O   ASN D 123 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 140 through 145
      removed outlier: 6.541A  pdb=" N   LYS D 143 " --> pdb=" O   PHE D 140 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 147 through 168
      removed outlier: 3.524A  pdb=" N   CYS D 151 " --> pdb=" O   VAL D 147 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL D 153 " --> pdb=" O   GLU D 149 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   TYR D 157 " --> pdb=" O   VAL D 153 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ARG D 160 " --> pdb=" O   ALA D 156 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ALA D 161 " --> pdb=" O   TYR D 157 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   THR D 168 " --> pdb=" O   GLY D 164 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 173 through 202
      removed outlier: 3.667A  pdb=" N   LEU D 177 " --> pdb=" O   SER D 173 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLU D 200 " --> pdb=" O   LEU D 196 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ARG D 201 " --> pdb=" O   HIS D 197 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   THR D 202 " --> pdb=" O   LEU D 198 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 213
    Processing helix  chain 'D' and resid 214 through 242
      removed outlier: 3.505A  pdb=" N   PHE D 238 " --> pdb=" O   GLY D 234 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLU D 239 " --> pdb=" O   LEU D 235 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLY D 242 " --> pdb=" O   PHE D 238 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 247 through 268
      removed outlier: 3.777A  pdb=" N   SER D 251 " --> pdb=" O   TRP D 247 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   MET D 252 " --> pdb=" O   PHE D 248 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   ILE D 253 " --> pdb=" O   ALA D 249 " (cutoff:3.500A)
      Proline residue:  D 254  - end of helix
      removed outlier: 3.650A  pdb=" N   VAL D 264 " --> pdb=" O   LEU D 260 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ASP D 265 " --> pdb=" O   ARG D 261 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLY D 268 " --> pdb=" O   VAL D 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 273 through 281
      removed outlier: 3.946A  pdb=" N   LEU D 279 " --> pdb=" O   GLU D 275 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ASP D 281 " --> pdb=" O   ILE D 277 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 281 through 302
      removed outlier: 3.860A  pdb=" N   GLN D 285 " --> pdb=" O   ASP D 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 18
      removed outlier: 3.668A  pdb=" N   VAL A  18 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 14 through 18'
    Processing helix  chain 'A' and resid 22 through 32
      removed outlier: 4.018A  pdb=" N   VAL A  27 " --> pdb=" O   ARG A  24 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LYS A  28 " --> pdb=" O   GLN A  25 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL A  30 " --> pdb=" O   VAL A  27 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LEU A  31 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL A  32 " --> pdb=" O   ASN A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 39
      removed outlier: 3.768A  pdb=" N   LEU A  37 " --> pdb=" O   LEU A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 77
      removed outlier: 3.889A  pdb=" N   SER A  56 " --> pdb=" O   LEU A  52 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   MET A  57 " --> pdb=" O   SER A  53 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   VAL A  60 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ALA A  65 " --> pdb=" O   VAL A  61 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   VAL A  75 " --> pdb=" O   LEU A  71 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ASP A  77 " --> pdb=" O   ASN A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 121
    Processing helix  chain 'A' and resid 123 through 139
      removed outlier: 3.575A  pdb=" N   VAL A 127 " --> pdb=" O   ASN A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 145
      removed outlier: 6.576A  pdb=" N   LYS A 143 " --> pdb=" O   PHE A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 168
      removed outlier: 3.523A  pdb=" N   CYS A 151 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL A 153 " --> pdb=" O   GLU A 149 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   TYR A 157 " --> pdb=" O   VAL A 153 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ARG A 160 " --> pdb=" O   ALA A 156 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ALA A 161 " --> pdb=" O   TYR A 157 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   THR A 168 " --> pdb=" O   GLY A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 202
      removed outlier: 3.667A  pdb=" N   LEU A 177 " --> pdb=" O   SER A 173 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLU A 200 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ARG A 201 " --> pdb=" O   HIS A 197 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   THR A 202 " --> pdb=" O   LEU A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 213
    Processing helix  chain 'A' and resid 214 through 242
      removed outlier: 3.504A  pdb=" N   PHE A 238 " --> pdb=" O   GLY A 234 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLU A 239 " --> pdb=" O   LEU A 235 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   GLY A 242 " --> pdb=" O   PHE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 268
      removed outlier: 3.777A  pdb=" N   SER A 251 " --> pdb=" O   TRP A 247 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   MET A 252 " --> pdb=" O   PHE A 248 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   ILE A 253 " --> pdb=" O   ALA A 249 " (cutoff:3.500A)
      Proline residue:  A 254  - end of helix
      removed outlier: 3.650A  pdb=" N   VAL A 264 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ASP A 265 " --> pdb=" O   ARG A 261 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLY A 268 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 281
      removed outlier: 3.807A  pdb=" N   LEU A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASP A 281 " --> pdb=" O   ILE A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 302
      removed outlier: 3.861A  pdb=" N   GLN A 285 " --> pdb=" O   ASP A 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 18
      removed outlier: 3.668A  pdb=" N   VAL B  18 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 14 through 18'
    Processing helix  chain 'B' and resid 22 through 32
      removed outlier: 4.017A  pdb=" N   VAL B  27 " --> pdb=" O   ARG B  24 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LYS B  28 " --> pdb=" O   GLN B  25 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL B  30 " --> pdb=" O   VAL B  27 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU B  31 " --> pdb=" O   LYS B  28 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL B  32 " --> pdb=" O   ASN B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 39
      removed outlier: 3.769A  pdb=" N   LEU B  37 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 77
      removed outlier: 3.889A  pdb=" N   SER B  56 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   MET B  57 " --> pdb=" O   SER B  53 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   VAL B  60 " --> pdb=" O   SER B  56 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ALA B  65 " --> pdb=" O   VAL B  61 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   VAL B  75 " --> pdb=" O   LEU B  71 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ASP B  77 " --> pdb=" O   ASN B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 121
    Processing helix  chain 'B' and resid 123 through 139
      removed outlier: 3.574A  pdb=" N   VAL B 127 " --> pdb=" O   ASN B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 145
      removed outlier: 6.530A  pdb=" N   LYS B 143 " --> pdb=" O   PHE B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 168
      removed outlier: 3.523A  pdb=" N   CYS B 151 " --> pdb=" O   VAL B 147 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL B 153 " --> pdb=" O   GLU B 149 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   TYR B 157 " --> pdb=" O   VAL B 153 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ARG B 160 " --> pdb=" O   ALA B 156 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ALA B 161 " --> pdb=" O   TYR B 157 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   THR B 168 " --> pdb=" O   GLY B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 202
      removed outlier: 3.668A  pdb=" N   LEU B 177 " --> pdb=" O   SER B 173 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLU B 200 " --> pdb=" O   LEU B 196 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ARG B 201 " --> pdb=" O   HIS B 197 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   THR B 202 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 213
    Processing helix  chain 'B' and resid 214 through 242
      removed outlier: 3.504A  pdb=" N   PHE B 238 " --> pdb=" O   GLY B 234 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLU B 239 " --> pdb=" O   LEU B 235 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   GLY B 242 " --> pdb=" O   PHE B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 268
      removed outlier: 3.777A  pdb=" N   SER B 251 " --> pdb=" O   TRP B 247 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   MET B 252 " --> pdb=" O   PHE B 248 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   ILE B 253 " --> pdb=" O   ALA B 249 " (cutoff:3.500A)
      Proline residue:  B 254  - end of helix
      removed outlier: 3.650A  pdb=" N   VAL B 264 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ASP B 265 " --> pdb=" O   ARG B 261 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLY B 268 " --> pdb=" O   VAL B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 281
      removed outlier: 3.882A  pdb=" N   LEU B 279 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASP B 281 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 302
      removed outlier: 3.860A  pdb=" N   GLN B 285 " --> pdb=" O   ASP B 281 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 83
      removed outlier: 5.010A  pdb=" N   ARG D  82 " --> pdb=" O   GLU D  79 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLU D  83 " --> pdb=" O   ALA D  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 83
      removed outlier: 5.010A  pdb=" N   ARG A  82 " --> pdb=" O   GLU A  79 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLU A  83 " --> pdb=" O   ALA A  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 83
      removed outlier: 5.010A  pdb=" N   ARG B  82 " --> pdb=" O   GLU B  79 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   GLU B  83 " --> pdb=" O   ALA B  80 " (cutoff:3.500A)

    421 hydrogen bonds defined for protein.
    1191 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.92

  Time building geometry restraints manager: 2.19 seconds

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

  Histogram of bond lengths:
        1.14 -     1.27: 1020
        1.27 -     1.40: 1782
        1.40 -     1.54: 4011
        1.54 -     1.67: 157
        1.67 -     1.81: 53
  Bond restraints: 7023
  Sorted by residual:
  bond pdb=" C1  PRP D 401 "
       pdb=" O4  PRP D 401 "
    ideal  model  delta    sigma   weight residual
    1.656  1.418  0.238 2.00e-02 2.50e+03 1.42e+02
  bond pdb=" C1  PRP A 401 "
       pdb=" O4  PRP A 401 "
    ideal  model  delta    sigma   weight residual
    1.656  1.419  0.237 2.00e-02 2.50e+03 1.41e+02
  bond pdb=" C1  PRP B 401 "
       pdb=" O4  PRP B 401 "
    ideal  model  delta    sigma   weight residual
    1.656  1.420  0.236 2.00e-02 2.50e+03 1.40e+02
  bond pdb=" C1  PRP A 401 "
       pdb=" C2  PRP A 401 "
    ideal  model  delta    sigma   weight residual
    1.327  1.509 -0.182 2.00e-02 2.50e+03 8.27e+01
  bond pdb=" C1  PRP B 401 "
       pdb=" C2  PRP B 401 "
    ideal  model  delta    sigma   weight residual
    1.327  1.508 -0.181 2.00e-02 2.50e+03 8.23e+01
  ... (remaining 7018 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.73: 9239
        2.73 -     5.46: 207
        5.46 -     8.19: 81
        8.19 -    10.92: 26
       10.92 -    13.64: 14
  Bond angle restraints: 9567
  Sorted by residual:
  angle pdb=" N   ILE D 206 "
        pdb=" CA  ILE D 206 "
        pdb=" C   ILE D 206 "
      ideal   model   delta    sigma   weight residual
     112.12   98.48   13.64 8.40e-01 1.42e+00 2.64e+02
  angle pdb=" N   ILE A 206 "
        pdb=" CA  ILE A 206 "
        pdb=" C   ILE A 206 "
      ideal   model   delta    sigma   weight residual
     112.12  100.15   11.97 8.40e-01 1.42e+00 2.03e+02
  angle pdb=" N   ILE B 206 "
        pdb=" CA  ILE B 206 "
        pdb=" C   ILE B 206 "
      ideal   model   delta    sigma   weight residual
     112.12  100.25   11.87 8.40e-01 1.42e+00 2.00e+02
  angle pdb=" N   ARG D 207 "
        pdb=" CA  ARG D 207 "
        pdb=" C   ARG D 207 "
      ideal   model   delta    sigma   weight residual
     111.30  121.24   -9.94 1.36e+00 5.41e-01 5.34e+01
  angle pdb=" N   ARG D 207 "
        pdb=" CA  ARG D 207 "
        pdb=" CB  ARG D 207 "
      ideal   model   delta    sigma   weight residual
     111.62  102.91    8.71 1.43e+00 4.89e-01 3.71e+01
  ... (remaining 9562 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.58: 3971
       31.58 -    63.15: 160
       63.15 -    94.73: 18
       94.73 -   126.31: 6
      126.31 -   157.89: 9
  Dihedral angle restraints: 4164
    sinusoidal: 1644
      harmonic: 2520
  Sorted by residual:
  dihedral pdb=" C   LYS B 143 "
           pdb=" N   LYS B 143 "
           pdb=" CA  LYS B 143 "
           pdb=" CB  LYS B 143 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.15  -12.45     0      2.50e+00 1.60e-01 2.48e+01
  dihedral pdb=" C03 PGW B 403 "
           pdb=" C01 PGW B 403 "
           pdb=" C02 PGW B 403 "
           pdb=" O03 PGW B 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.65   93.24 -157.89     1      3.00e+01 1.11e-03 2.05e+01
  dihedral pdb=" C03 PGW A 403 "
           pdb=" C01 PGW A 403 "
           pdb=" C02 PGW A 403 "
           pdb=" O03 PGW A 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.65   93.23 -157.88     1      3.00e+01 1.11e-03 2.05e+01
  ... (remaining 4161 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.111: 1084
       0.111 -    0.223: 33
       0.223 -    0.334: 2
       0.334 -    0.446: 6
       0.446 -    0.557: 3
  Chirality restraints: 1128
  Sorted by residual:
  chirality pdb=" C02 PGW B 403 "
            pdb=" C01 PGW B 403 "
            pdb=" C03 PGW B 403 "
            pdb=" O01 PGW B 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.36    2.91   -0.56 2.00e-01 2.50e+01 7.76e+00
  chirality pdb=" C02 PGW D 403 "
            pdb=" C01 PGW D 403 "
            pdb=" C03 PGW D 403 "
            pdb=" O01 PGW D 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.36    2.91   -0.56 2.00e-01 2.50e+01 7.72e+00
  chirality pdb=" C02 PGW A 403 "
            pdb=" C01 PGW A 403 "
            pdb=" C03 PGW A 403 "
            pdb=" O01 PGW A 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.36    2.91   -0.55 2.00e-01 2.50e+01 7.69e+00
  ... (remaining 1125 not shown)

  Planarity restraints: 1143
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 169 "    0.013 2.00e-02 2.50e+03   2.73e-02 7.47e+00
        pdb=" C   LYS B 169 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   LYS B 169 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ILE B 170 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 169 "   -0.013 2.00e-02 2.50e+03   2.63e-02 6.93e+00
        pdb=" C   LYS A 169 "    0.046 2.00e-02 2.50e+03
        pdb=" O   LYS A 169 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ILE A 170 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR D 168 "    0.013 2.00e-02 2.50e+03   2.55e-02 6.48e+00
        pdb=" C   THR D 168 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   THR D 168 "    0.016 2.00e-02 2.50e+03
        pdb=" N   LYS D 169 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1140 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.35: 10
        2.35 -     2.99: 3405
        2.99 -     3.63: 9498
        3.63 -     4.26: 14914
        4.26 -     4.90: 25546
  Nonbonded interactions: 53373
  Sorted by model distance:
  nonbonded pdb=" O3B PRP A 401 "
            pdb="MG    MG A 402 "
     model   vdw
     1.717 2.170
  nonbonded pdb=" O3B PRP B 401 "
            pdb="MG    MG B 402 "
     model   vdw
     1.821 2.170
  nonbonded pdb=" O3B PRP D 401 "
            pdb="MG    MG D 402 "
     model   vdw
     1.836 2.170
  nonbonded pdb=" O1A PRP A 401 "
            pdb="MG    MG A 402 "
     model   vdw
     1.989 2.170
  nonbonded pdb=" O1A PRP D 401 "
            pdb="MG    MG D 402 "
     model   vdw
     2.000 2.170
  ... (remaining 53368 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 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.590
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.580
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.238   7023  Z= 0.703
  Angle     :  1.193  13.645   9567  Z= 0.641
  Chirality :  0.061   0.557   1128
  Planarity :  0.005   0.034   1143
  Dihedral  : 19.317 157.885   2550
  Min Nonbonded Distance : 1.717

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.90 %
    Favored  : 88.10 %
  Cbeta Deviations :  0.12 %
  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: -2.54 (0.24), residues: 864
  helix: -1.07 (0.18), residues: 663
  sheet:  None (None), residues: 0
  loop : -3.37 (0.29), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 222 
 HIS   0.005   0.002   HIS D 197 
 PHE   0.014   0.002   PHE D 182 
 TYR   0.016   0.002   TYR A 217 
 ARG   0.005   0.000   ARG D 201 

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.694 
Fit side-chains
REVERT: D  212 SER cc_start: 0.8357 (m) cc_final: 0.8044 (p)
REVERT: B  187 MET cc_start: 0.8118 (mmt) cc_final: 0.7898 (mmt)
REVERT: B  270 LEU cc_start: 0.7196 (mt) cc_final: 0.6994 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 1.1426
  time to fit residues: 114.1454
Evaluate side-chains
  75 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 65 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 22 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 68 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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: 0.8112
moved from start:          0.1310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7023  Z= 0.193
  Angle     :  0.594   7.992   9567  Z= 0.302
  Chirality :  0.040   0.196   1128
  Planarity :  0.004   0.026   1143
  Dihedral  : 18.166 148.886   1176
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 13.39 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.67 (0.27), residues: 864
  helix:  0.18 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -2.35 (0.35), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 222 
 HIS   0.004   0.001   HIS D 197 
 PHE   0.012   0.002   PHE D 182 
 TYR   0.030   0.002   TYR D 213 
 ARG   0.002   0.000   ARG B 201 

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.827 
Fit side-chains
REVERT: D   45 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6214 (ttt90)
REVERT: A  142 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8162 (mp)
REVERT: B  187 MET cc_start: 0.7975 (mmt) cc_final: 0.7746 (mmt)
  outliers start: 19
  outliers final: 6
  residues processed: 84
  average time/residue: 1.0942
  time to fit residues: 97.7041
Evaluate side-chains
  80 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   45 ARG
Chi-restraints excluded: chain D residue   57 MET
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   56 SER
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue  292 ILE
Chi-restraints excluded: chain B residue  295 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 65 optimal weight:    7.9990
   chunk 53 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 79 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 78 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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: 0.8091
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7023  Z= 0.170
  Angle     :  0.556   7.620   9567  Z= 0.283
  Chirality :  0.039   0.188   1128
  Planarity :  0.003   0.023   1143
  Dihedral  : 16.908 150.724   1176
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 15.33 %
    Favored  : 81.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.66 (0.28), residues: 864
  helix:  1.10 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -1.39 (0.37), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 222 
 HIS   0.003   0.001   HIS D 197 
 PHE   0.011   0.002   PHE D 182 
 TYR   0.021   0.001   TYR D 213 
 ARG   0.003   0.000   ARG B 201 

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.751 
Fit side-chains
REVERT: D   45 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6154 (ttt90)
REVERT: D   62 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.7422 (t80)
REVERT: A   45 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6819 (ttt90)
REVERT: A   62 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8141 (t80)
REVERT: A  142 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8085 (mp)
REVERT: B  187 MET cc_start: 0.7973 (mmt) cc_final: 0.7755 (mmt)
  outliers start: 20
  outliers final: 6
  residues processed: 90
  average time/residue: 0.9572
  time to fit residues: 91.4300
Evaluate side-chains
  87 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   45 ARG
Chi-restraints excluded: chain D residue   62 PHE
Chi-restraints excluded: chain A residue   45 ARG
Chi-restraints excluded: chain A residue   56 SER
Chi-restraints excluded: chain A residue   62 PHE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   62 PHE
Chi-restraints excluded: chain B residue  295 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 78 optimal weight:    0.2980
   chunk 59 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 8 optimal weight:    0.3980
   chunk 37 optimal weight:    0.0010
   chunk 53 optimal weight:    0.5980
   chunk 79 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    0.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 197 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   7023  Z= 0.128
  Angle     :  0.513   8.813   9567  Z= 0.258
  Chirality :  0.037   0.172   1128
  Planarity :  0.003   0.021   1143
  Dihedral  : 15.761 150.149   1176
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 16.07 %
    Favored  : 80.65 %
  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:  1.38 (0.29), residues: 864
  helix:  1.60 (0.21), residues: 633
  sheet:  None (None), residues: 0
  loop : -0.98 (0.39), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP D 222 
 HIS   0.003   0.001   HIS A 197 
 PHE   0.008   0.001   PHE D 255 
 TYR   0.013   0.001   TYR D 213 
 ARG   0.002   0.000   ARG B 201 

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 0.745 
Fit side-chains
REVERT: D   45 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6178 (ttt90)
REVERT: D   62 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.7354 (t80)
REVERT: A   45 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6623 (ttt90)
REVERT: A   62 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8291 (t80)
REVERT: A  142 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8053 (mp)
REVERT: B   56 SER cc_start: 0.8196 (OUTLIER) cc_final: 0.7973 (p)
REVERT: B  187 MET cc_start: 0.7924 (mmt) cc_final: 0.7692 (mmt)
REVERT: B  301 PHE cc_start: 0.7870 (m-10) cc_final: 0.7639 (m-80)
  outliers start: 22
  outliers final: 3
  residues processed: 88
  average time/residue: 1.2137
  time to fit residues: 113.1387
Evaluate side-chains
  81 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   45 ARG
Chi-restraints excluded: chain D residue   62 PHE
Chi-restraints excluded: chain A residue   45 ARG
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   62 PHE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   62 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 58 optimal weight:    7.9990
   chunk 0 optimal weight:    4.9990
   chunk 42 optimal weight:    0.4980
   chunk 75 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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: 0.8075
moved from start:          0.2014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7023  Z= 0.163
  Angle     :  0.536   9.412   9567  Z= 0.272
  Chirality :  0.038   0.187   1128
  Planarity :  0.003   0.022   1143
  Dihedral  : 15.761 148.536   1176
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 17.11 %
    Favored  : 80.36 %
  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:  1.42 (0.29), residues: 864
  helix:  1.60 (0.21), residues: 633
  sheet:  None (None), residues: 0
  loop : -0.87 (0.39), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP B 222 
 HIS   0.002   0.001   HIS D 197 
 PHE   0.012   0.002   PHE D 182 
 TYR   0.015   0.001   TYR D 213 
 ARG   0.001   0.000   ARG B 201 

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.700 
Fit side-chains
REVERT: D   45 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6178 (ttt90)
REVERT: D   62 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.7410 (t80)
REVERT: A   45 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6774 (ttt90)
REVERT: A   62 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8129 (t80)
REVERT: A  142 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8069 (mp)
REVERT: B  187 MET cc_start: 0.7967 (mmt) cc_final: 0.7720 (mmt)
REVERT: B  301 PHE cc_start: 0.7889 (m-10) cc_final: 0.7652 (m-80)
  outliers start: 17
  outliers final: 7
  residues processed: 82
  average time/residue: 1.1179
  time to fit residues: 97.2212
Evaluate side-chains
  82 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   45 ARG
Chi-restraints excluded: chain D residue   62 PHE
Chi-restraints excluded: chain D residue  134 MET
Chi-restraints excluded: chain A residue   45 ARG
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   62 PHE
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   62 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0000
   chunk 69 optimal weight:    0.8980
   chunk 38 optimal weight:    0.2980
   chunk 6 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.4984

-------------------------------------------------------------------------------
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: 0.8041
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7023  Z= 0.142
  Angle     :  0.520   9.850   9567  Z= 0.260
  Chirality :  0.038   0.179   1128
  Planarity :  0.003   0.021   1143
  Dihedral  : 15.180 145.402   1176
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 17.11 %
    Favored  : 80.51 %
  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:  1.71 (0.29), residues: 864
  helix:  1.80 (0.21), residues: 633
  sheet:  None (None), residues: 0
  loop : -0.70 (0.40), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 222 
 HIS   0.001   0.000   HIS D 197 
 PHE   0.009   0.001   PHE A 255 
 TYR   0.012   0.001   TYR D 213 
 ARG   0.001   0.000   ARG D  24 

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.726 
Fit side-chains
REVERT: D   45 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6195 (ttt90)
REVERT: D   62 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.7374 (t80)
REVERT: D  270 LEU cc_start: 0.7169 (mt) cc_final: 0.6948 (mt)
REVERT: A   45 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6671 (ttt90)
REVERT: A   62 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8215 (t80)
REVERT: A  142 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8070 (mp)
REVERT: B   56 SER cc_start: 0.8169 (OUTLIER) cc_final: 0.7933 (p)
REVERT: B  187 MET cc_start: 0.7978 (mmt) cc_final: 0.7738 (mmt)
REVERT: B  301 PHE cc_start: 0.7827 (m-10) cc_final: 0.7598 (m-80)
  outliers start: 16
  outliers final: 6
  residues processed: 81
  average time/residue: 1.1575
  time to fit residues: 99.4010
Evaluate side-chains
  83 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   45 ARG
Chi-restraints excluded: chain D residue   62 PHE
Chi-restraints excluded: chain A residue   45 ARG
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   62 PHE
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   62 PHE
Chi-restraints excluded: chain B residue  208 LYS
Chi-restraints excluded: chain B residue  295 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 61 optimal weight:    6.9990
   chunk 70 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0070
   overall best weight:    0.5598

-------------------------------------------------------------------------------
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: 0.8055
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7023  Z= 0.148
  Angle     :  0.524  10.267   9567  Z= 0.263
  Chirality :  0.038   0.184   1128
  Planarity :  0.003   0.021   1143
  Dihedral  : 14.974 144.027   1176
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 18.01 %
    Favored  : 79.76 %
  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:  1.77 (0.29), residues: 864
  helix:  1.75 (0.21), residues: 639
  sheet:  None (None), residues: 0
  loop : -0.45 (0.41), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B 222 
 HIS   0.001   0.000   HIS B 197 
 PHE   0.010   0.001   PHE D 182 
 TYR   0.012   0.001   TYR D 213 
 ARG   0.001   0.000   ARG D  24 

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.717 
Fit side-chains
REVERT: D   45 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6357 (ttt90)
REVERT: D   62 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.7393 (t80)
REVERT: D  270 LEU cc_start: 0.7176 (mt) cc_final: 0.6961 (mt)
REVERT: A   45 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6594 (ttt90)
REVERT: A   62 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8233 (t80)
REVERT: A  142 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8053 (mp)
REVERT: B  187 MET cc_start: 0.7974 (mmt) cc_final: 0.7733 (mmt)
REVERT: B  301 PHE cc_start: 0.7812 (m-10) cc_final: 0.7578 (m-80)
  outliers start: 15
  outliers final: 5
  residues processed: 82
  average time/residue: 1.1294
  time to fit residues: 98.1488
Evaluate side-chains
  80 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   45 ARG
Chi-restraints excluded: chain D residue   62 PHE
Chi-restraints excluded: chain D residue  134 MET
Chi-restraints excluded: chain A residue   45 ARG
Chi-restraints excluded: chain A residue   62 PHE
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   62 PHE
Chi-restraints excluded: chain B residue  295 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 53 optimal weight:    0.1980
   chunk 57 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 65 optimal weight:   10.0000
   chunk 76 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A 197 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7023  Z= 0.178
  Angle     :  0.560  10.953   9567  Z= 0.279
  Chirality :  0.039   0.193   1128
  Planarity :  0.003   0.022   1143
  Dihedral  : 15.039 142.602   1176
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 18.15 %
    Favored  : 79.76 %
  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:  1.66 (0.28), residues: 864
  helix:  1.65 (0.20), residues: 639
  sheet:  None (None), residues: 0
  loop : -0.41 (0.40), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B 222 
 HIS   0.003   0.001   HIS A 197 
 PHE   0.013   0.002   PHE D 182 
 TYR   0.014   0.001   TYR D 213 
 ARG   0.001   0.000   ARG D  24 

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.702 
Fit side-chains
REVERT: D   45 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6317 (ttt90)
REVERT: D   62 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.7425 (t80)
REVERT: D  270 LEU cc_start: 0.7211 (mt) cc_final: 0.6991 (mt)
REVERT: A   45 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6508 (ttt90)
REVERT: A   62 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8220 (t80)
REVERT: A  142 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8082 (mp)
REVERT: B  301 PHE cc_start: 0.7842 (m-10) cc_final: 0.7597 (m-80)
  outliers start: 14
  outliers final: 6
  residues processed: 79
  average time/residue: 1.1403
  time to fit residues: 95.5236
Evaluate side-chains
  81 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   45 ARG
Chi-restraints excluded: chain D residue   62 PHE
Chi-restraints excluded: chain A residue   45 ARG
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   62 PHE
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain B residue   62 PHE
Chi-restraints excluded: chain B residue  295 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 73 optimal weight:    0.2980
   chunk 77 optimal weight:    6.9990
   chunk 51 optimal weight:    0.6980
   chunk 82 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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: 0.8074
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7023  Z= 0.167
  Angle     :  0.543  10.915   9567  Z= 0.272
  Chirality :  0.038   0.191   1128
  Planarity :  0.003   0.022   1143
  Dihedral  : 14.866 139.743   1176
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 18.45 %
    Favored  : 79.76 %
  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:  1.80 (0.28), residues: 864
  helix:  1.75 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -0.31 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B 222 
 HIS   0.002   0.000   HIS D 197 
 PHE   0.012   0.002   PHE D 182 
 TYR   0.013   0.001   TYR D 213 
 ARG   0.001   0.000   ARG D  24 

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.704 
Fit side-chains
REVERT: D   45 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6314 (ttt90)
REVERT: D   62 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.7414 (t80)
REVERT: D  270 LEU cc_start: 0.7188 (mt) cc_final: 0.6975 (mt)
REVERT: A   45 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6526 (ttt90)
REVERT: A   62 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8223 (t80)
REVERT: A  142 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8063 (mp)
REVERT: B  301 PHE cc_start: 0.7822 (m-10) cc_final: 0.7571 (m-80)
  outliers start: 12
  outliers final: 6
  residues processed: 79
  average time/residue: 1.0939
  time to fit residues: 91.7736
Evaluate side-chains
  81 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   45 ARG
Chi-restraints excluded: chain D residue   62 PHE
Chi-restraints excluded: chain A residue   45 ARG
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   62 PHE
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain B residue   62 PHE
Chi-restraints excluded: chain B residue  295 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 79 optimal weight:    0.6980
   chunk 69 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 53 optimal weight:    0.5980
   chunk 42 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0980
   chunk 73 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 63 optimal weight:    0.4980
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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: 0.8049
moved from start:          0.2296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7023  Z= 0.147
  Angle     :  0.542  10.531   9567  Z= 0.268
  Chirality :  0.038   0.181   1128
  Planarity :  0.003   0.022   1143
  Dihedral  : 14.572 136.488   1176
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 18.45 %
    Favored  : 79.61 %
  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:  2.02 (0.29), residues: 864
  helix:  1.93 (0.21), residues: 633
  sheet:  None (None), residues: 0
  loop : -0.28 (0.40), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 222 
 HIS   0.001   0.000   HIS B 197 
 PHE   0.009   0.001   PHE A 182 
 TYR   0.012   0.001   TYR D 213 
 ARG   0.002   0.000   ARG D  24 

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.707 
Fit side-chains
REVERT: D   45 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6443 (ttt90)
REVERT: D   62 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.7396 (t80)
REVERT: D  270 LEU cc_start: 0.7185 (mt) cc_final: 0.6978 (mt)
REVERT: A   45 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6557 (ttt90)
REVERT: A   62 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8210 (t80)
REVERT: A  142 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8070 (mp)
REVERT: B  301 PHE cc_start: 0.7774 (m-10) cc_final: 0.7542 (m-80)
  outliers start: 13
  outliers final: 7
  residues processed: 79
  average time/residue: 1.1324
  time to fit residues: 94.9335
Evaluate side-chains
  80 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   45 ARG
Chi-restraints excluded: chain D residue   62 PHE
Chi-restraints excluded: chain A residue   45 ARG
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   62 PHE
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain B residue   62 PHE
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  295 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 60 optimal weight:    0.1980
   chunk 3 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3757 r_free = 0.3757 target = 0.159933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.100035 restraints weight = 6937.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 2.10
r_work: 0.2888 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2754 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7023  Z= 0.175
  Angle     :  0.552  11.018   9567  Z= 0.276
  Chirality :  0.039   0.192   1128
  Planarity :  0.003   0.022   1143
  Dihedral  : 14.617 135.323   1176
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 18.60 %
    Favored  : 79.61 %
  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:  1.86 (0.28), residues: 864
  helix:  1.75 (0.20), residues: 639
  sheet:  None (None), residues: 0
  loop : -0.18 (0.41), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B 222 
 HIS   0.002   0.000   HIS B 197 
 PHE   0.013   0.002   PHE D 182 
 TYR   0.014   0.001   TYR D 213 
 ARG   0.001   0.000   ARG D  24 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2377.59 seconds
wall clock time: 50 minutes 3.63 seconds (3003.63 seconds total)