Starting phenix.real_space_refine
on Sat Nov 16 23:34:09 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f34_28831/11_2024/8f34_28831.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f34_28831/11_2024/8f34_28831.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f34_28831/11_2024/8f34_28831.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f34_28831/11_2024/8f34_28831.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f34_28831/11_2024/8f34_28831.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f34_28831/11_2024/8f34_28831.cif"
  }
  resolution = 3.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    8180      2.51       5
     N    2085      2.21       5
     O    2250      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 12545
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'3CN': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 5.73, per 1000 atoms: 0.46
  Number of scatterers: 12545
  At special positions: 0
  Unit cell: (88.038, 88.038, 122.859, 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      30     16.00
     O    2250      8.00
     N    2085      7.00
     C    8180      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: 3.64
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2910

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 10 sheets defined
      31.3% alpha, 32.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.42
  Creating SS restraints...
    Processing helix  chain 'E' and resid 62 through 70
      removed outlier: 3.864A  pdb=" N   TRP E  66 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 201 through 208
    Processing helix  chain 'E' and resid 208 through 221
      removed outlier: 3.819A  pdb=" N   LEU E 212 " --> pdb=" O   PHE E 208 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 222 through 225
    Processing helix  chain 'E' and resid 227 through 245
    Processing helix  chain 'E' and resid 260 through 286
    Processing helix  chain 'E' and resid 303 through 317
    Processing helix  chain 'D' and resid 62 through 70
      removed outlier: 3.864A  pdb=" N   TRP D  66 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 201 through 208
    Processing helix  chain 'D' and resid 208 through 221
      removed outlier: 3.819A  pdb=" N   LEU D 212 " --> pdb=" O   PHE D 208 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 222 through 225
    Processing helix  chain 'D' and resid 227 through 245
    Processing helix  chain 'D' and resid 260 through 286
    Processing helix  chain 'D' and resid 303 through 317
    Processing helix  chain 'C' and resid 62 through 70
      removed outlier: 3.863A  pdb=" N   TRP C  66 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 201 through 208
    Processing helix  chain 'C' and resid 208 through 221
      removed outlier: 3.819A  pdb=" N   LEU C 212 " --> pdb=" O   PHE C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 225
    Processing helix  chain 'C' and resid 227 through 245
    Processing helix  chain 'C' and resid 260 through 286
    Processing helix  chain 'C' and resid 303 through 317
    Processing helix  chain 'B' and resid 62 through 70
      removed outlier: 3.863A  pdb=" N   TRP B  66 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 208
    Processing helix  chain 'B' and resid 208 through 221
      removed outlier: 3.819A  pdb=" N   LEU B 212 " --> pdb=" O   PHE B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 225
    Processing helix  chain 'B' and resid 227 through 245
    Processing helix  chain 'B' and resid 260 through 286
    Processing helix  chain 'B' and resid 303 through 317
    Processing helix  chain 'A' and resid 62 through 70
      removed outlier: 3.864A  pdb=" N   TRP A  66 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 208
    Processing helix  chain 'A' and resid 208 through 221
      removed outlier: 3.819A  pdb=" N   LEU A 212 " --> pdb=" O   PHE A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 227 through 245
    Processing helix  chain 'A' and resid 260 through 286
    Processing helix  chain 'A' and resid 303 through 317
    Processing sheet with id=AA1, first strand: chain 'E' and resid 56 through 58
      removed outlier: 4.289A  pdb=" N   SER E 109 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   SER E  84 " --> pdb=" O   LEU E 107 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   LEU E 107 " --> pdb=" O   SER E  84 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ASP E  86 " --> pdb=" O   ARG E 105 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ARG E 105 " --> pdb=" O   ASP E  86 " (cutoff:3.500A)
      removed outlier: 8.311A  pdb=" N   GLY E  88 " --> pdb=" O   ASN E 103 " (cutoff:3.500A)
      removed outlier: 10.358A  pdb=" N   ASN E 103 " --> pdb=" O   GLY E  88 " (cutoff:3.500A)
      removed outlier: 9.936A  pdb=" N   LYS E  90 " --> pdb=" O   ILE E 101 " (cutoff:3.500A)
      removed outlier: 11.161A  pdb=" N   ILE E 101 " --> pdb=" O   LYS E  90 " (cutoff:3.500A)
      removed outlier: 9.870A  pdb=" N   LEU E  92 " --> pdb=" O   ARG E  99 " (cutoff:3.500A)
      removed outlier: 10.904A  pdb=" N   ARG E  99 " --> pdb=" O   LEU E  92 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   THR E  32 " --> pdb=" O   GLY E  25 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   GLY E  25 " --> pdb=" O   THR E  32 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   LYS E  34 " --> pdb=" O   ILE E  23 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   ILE E  23 " --> pdb=" O   LYS E  34 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ASP E  36 " --> pdb=" O   ASN E  21 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   THR E  44 " --> pdb=" O   ASP E  13 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ASP E  13 " --> pdb=" O   THR E  44 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   VAL E  12 " --> pdb=" O   ARG E 141 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   SER E 143 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   VAL E  14 " --> pdb=" O   SER E 143 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ILE E 145 " --> pdb=" O   VAL E  14 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   VAL E  16 " --> pdb=" O   ILE E 145 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   VAL E 147 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ILE E  18 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.628A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   PHE E 188 " --> pdb=" O   SER E 171 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   SER E 171 " --> pdb=" O   PHE E 188 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ARG E 190 " --> pdb=" O   HIS E 169 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   HIS E 169 " --> pdb=" O   ARG E 190 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   THR E 192 " --> pdb=" O   SER E 167 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   SER E 167 " --> pdb=" O   THR E 192 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   ARG E 194 " --> pdb=" O   LYS E 165 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   LYS E 165 " --> pdb=" O   ARG E 194 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   ASP E 196 " --> pdb=" O   ARG E 163 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 56 through 58
      removed outlier: 4.289A  pdb=" N   SER D 109 " --> pdb=" O   VAL D  82 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   SER D  84 " --> pdb=" O   LEU D 107 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   LEU D 107 " --> pdb=" O   SER D  84 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ASP D  86 " --> pdb=" O   ARG D 105 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ARG D 105 " --> pdb=" O   ASP D  86 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   GLY D  88 " --> pdb=" O   ASN D 103 " (cutoff:3.500A)
      removed outlier: 10.359A  pdb=" N   ASN D 103 " --> pdb=" O   GLY D  88 " (cutoff:3.500A)
      removed outlier: 9.936A  pdb=" N   LYS D  90 " --> pdb=" O   ILE D 101 " (cutoff:3.500A)
      removed outlier: 11.161A  pdb=" N   ILE D 101 " --> pdb=" O   LYS D  90 " (cutoff:3.500A)
      removed outlier: 9.869A  pdb=" N   LEU D  92 " --> pdb=" O   ARG D  99 " (cutoff:3.500A)
      removed outlier: 10.904A  pdb=" N   ARG D  99 " --> pdb=" O   LEU D  92 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   THR D  32 " --> pdb=" O   GLY D  25 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   GLY D  25 " --> pdb=" O   THR D  32 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   LYS D  34 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   ILE D  23 " --> pdb=" O   LYS D  34 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ASP D  36 " --> pdb=" O   ASN D  21 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   THR D  44 " --> pdb=" O   ASP D  13 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ASP D  13 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   VAL D  12 " --> pdb=" O   ARG D 141 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   SER D 143 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   VAL D  14 " --> pdb=" O   SER D 143 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   ILE D 145 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   VAL D  16 " --> pdb=" O   ILE D 145 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   VAL D 147 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ILE D  18 " --> pdb=" O   VAL D 147 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.628A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   PHE D 188 " --> pdb=" O   SER D 171 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   SER D 171 " --> pdb=" O   PHE D 188 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ARG D 190 " --> pdb=" O   HIS D 169 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   HIS D 169 " --> pdb=" O   ARG D 190 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   THR D 192 " --> pdb=" O   SER D 167 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   SER D 167 " --> pdb=" O   THR D 192 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   ARG D 194 " --> pdb=" O   LYS D 165 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   LYS D 165 " --> pdb=" O   ARG D 194 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   ASP D 196 " --> pdb=" O   ARG D 163 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 56 through 58
      removed outlier: 4.289A  pdb=" N   SER C 109 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   SER C  84 " --> pdb=" O   LEU C 107 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   LEU C 107 " --> pdb=" O   SER C  84 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ASP C  86 " --> pdb=" O   ARG C 105 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ARG C 105 " --> pdb=" O   ASP C  86 " (cutoff:3.500A)
      removed outlier: 8.311A  pdb=" N   GLY C  88 " --> pdb=" O   ASN C 103 " (cutoff:3.500A)
      removed outlier: 10.357A  pdb=" N   ASN C 103 " --> pdb=" O   GLY C  88 " (cutoff:3.500A)
      removed outlier: 9.936A  pdb=" N   LYS C  90 " --> pdb=" O   ILE C 101 " (cutoff:3.500A)
      removed outlier: 11.162A  pdb=" N   ILE C 101 " --> pdb=" O   LYS C  90 " (cutoff:3.500A)
      removed outlier: 9.869A  pdb=" N   LEU C  92 " --> pdb=" O   ARG C  99 " (cutoff:3.500A)
      removed outlier: 10.904A  pdb=" N   ARG C  99 " --> pdb=" O   LEU C  92 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   THR C  32 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   GLY C  25 " --> pdb=" O   THR C  32 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   LYS C  34 " --> pdb=" O   ILE C  23 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   ILE C  23 " --> pdb=" O   LYS C  34 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   ASP C  36 " --> pdb=" O   ASN C  21 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   THR C  44 " --> pdb=" O   ASP C  13 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ASP C  13 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   VAL C  12 " --> pdb=" O   ARG C 141 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   SER C 143 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   VAL C  14 " --> pdb=" O   SER C 143 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ILE C 145 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   VAL C  16 " --> pdb=" O   ILE C 145 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   VAL C 147 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ILE C  18 " --> pdb=" O   VAL C 147 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.629A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   PHE C 188 " --> pdb=" O   SER C 171 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   SER C 171 " --> pdb=" O   PHE C 188 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ARG C 190 " --> pdb=" O   HIS C 169 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   HIS C 169 " --> pdb=" O   ARG C 190 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   THR C 192 " --> pdb=" O   SER C 167 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   SER C 167 " --> pdb=" O   THR C 192 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   ARG C 194 " --> pdb=" O   LYS C 165 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   LYS C 165 " --> pdb=" O   ARG C 194 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   ASP C 196 " --> pdb=" O   ARG C 163 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 56 through 58
      removed outlier: 4.289A  pdb=" N   SER B 109 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   SER B  84 " --> pdb=" O   LEU B 107 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   LEU B 107 " --> pdb=" O   SER B  84 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ASP B  86 " --> pdb=" O   ARG B 105 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ARG B 105 " --> pdb=" O   ASP B  86 " (cutoff:3.500A)
      removed outlier: 8.311A  pdb=" N   GLY B  88 " --> pdb=" O   ASN B 103 " (cutoff:3.500A)
      removed outlier: 10.357A  pdb=" N   ASN B 103 " --> pdb=" O   GLY B  88 " (cutoff:3.500A)
      removed outlier: 9.936A  pdb=" N   LYS B  90 " --> pdb=" O   ILE B 101 " (cutoff:3.500A)
      removed outlier: 11.162A  pdb=" N   ILE B 101 " --> pdb=" O   LYS B  90 " (cutoff:3.500A)
      removed outlier: 9.870A  pdb=" N   LEU B  92 " --> pdb=" O   ARG B  99 " (cutoff:3.500A)
      removed outlier: 10.904A  pdb=" N   ARG B  99 " --> pdb=" O   LEU B  92 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   THR B  32 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   GLY B  25 " --> pdb=" O   THR B  32 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   LYS B  34 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   ILE B  23 " --> pdb=" O   LYS B  34 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ASP B  36 " --> pdb=" O   ASN B  21 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   THR B  44 " --> pdb=" O   ASP B  13 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   ASP B  13 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   VAL B  12 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   SER B 143 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   VAL B  14 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   ILE B 145 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   VAL B  16 " --> pdb=" O   ILE B 145 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   VAL B 147 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ILE B  18 " --> pdb=" O   VAL B 147 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.628A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   PHE B 188 " --> pdb=" O   SER B 171 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   SER B 171 " --> pdb=" O   PHE B 188 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ARG B 190 " --> pdb=" O   HIS B 169 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   HIS B 169 " --> pdb=" O   ARG B 190 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   THR B 192 " --> pdb=" O   SER B 167 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   SER B 167 " --> pdb=" O   THR B 192 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   ARG B 194 " --> pdb=" O   LYS B 165 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   LYS B 165 " --> pdb=" O   ARG B 194 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   ASP B 196 " --> pdb=" O   ARG B 163 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 56 through 58
      removed outlier: 4.289A  pdb=" N   SER A 109 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   SER A  84 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   LEU A 107 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ASP A  86 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ARG A 105 " --> pdb=" O   ASP A  86 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   GLY A  88 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
      removed outlier: 10.358A  pdb=" N   ASN A 103 " --> pdb=" O   GLY A  88 " (cutoff:3.500A)
      removed outlier: 9.935A  pdb=" N   LYS A  90 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 11.160A  pdb=" N   ILE A 101 " --> pdb=" O   LYS A  90 " (cutoff:3.500A)
      removed outlier: 9.869A  pdb=" N   LEU A  92 " --> pdb=" O   ARG A  99 " (cutoff:3.500A)
      removed outlier: 10.904A  pdb=" N   ARG A  99 " --> pdb=" O   LEU A  92 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   THR A  32 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   GLY A  25 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   LYS A  34 " --> pdb=" O   ILE A  23 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   ILE A  23 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ASP A  36 " --> pdb=" O   ASN A  21 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   THR A  44 " --> pdb=" O   ASP A  13 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ASP A  13 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   VAL A  12 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   SER A 143 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   VAL A  14 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   ILE A 145 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   VAL A  16 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   VAL A 147 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   ILE A  18 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.629A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   PHE A 188 " --> pdb=" O   SER A 171 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   SER A 171 " --> pdb=" O   PHE A 188 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   ARG A 190 " --> pdb=" O   HIS A 169 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   HIS A 169 " --> pdb=" O   ARG A 190 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   THR A 192 " --> pdb=" O   SER A 167 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   SER A 167 " --> pdb=" O   THR A 192 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   ARG A 194 " --> pdb=" O   LYS A 165 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   LYS A 165 " --> pdb=" O   ARG A 194 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   ASP A 196 " --> pdb=" O   ARG A 163 " (cutoff:3.500A)

    530 hydrogen bonds defined for protein.
    1545 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: 3.66

  Time building geometry restraints manager: 3.90 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3892
        1.34 -     1.46: 2331
        1.46 -     1.57: 6607
        1.57 -     1.69: 0
        1.69 -     1.81: 50
  Bond restraints: 12880
  Sorted by residual:
  bond pdb=" CA  TRP C 160 "
       pdb=" C   TRP C 160 "
    ideal  model  delta    sigma   weight residual
    1.526  1.507  0.020 1.03e-02 9.43e+03 3.64e+00
  bond pdb=" CA  TRP E 160 "
       pdb=" C   TRP E 160 "
    ideal  model  delta    sigma   weight residual
    1.526  1.507  0.019 1.03e-02 9.43e+03 3.46e+00
  bond pdb=" CA  TRP A 160 "
       pdb=" C   TRP A 160 "
    ideal  model  delta    sigma   weight residual
    1.526  1.507  0.019 1.03e-02 9.43e+03 3.43e+00
  bond pdb=" CA  TRP B 160 "
       pdb=" C   TRP B 160 "
    ideal  model  delta    sigma   weight residual
    1.526  1.507  0.019 1.03e-02 9.43e+03 3.40e+00
  bond pdb=" CA  TRP D 160 "
       pdb=" C   TRP D 160 "
    ideal  model  delta    sigma   weight residual
    1.526  1.507  0.019 1.03e-02 9.43e+03 3.39e+00
  ... (remaining 12875 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 16973
        1.86 -     3.72: 477
        3.72 -     5.58: 50
        5.58 -     7.45: 35
        7.45 -     9.31: 10
  Bond angle restraints: 17545
  Sorted by residual:
  angle pdb=" C   ASN B  60 "
        pdb=" N   THR B  61 "
        pdb=" CA  THR B  61 "
      ideal   model   delta    sigma   weight residual
     121.54  130.85   -9.31 1.91e+00 2.74e-01 2.37e+01
  angle pdb=" C   ASN E  60 "
        pdb=" N   THR E  61 "
        pdb=" CA  THR E  61 "
      ideal   model   delta    sigma   weight residual
     121.54  130.79   -9.25 1.91e+00 2.74e-01 2.35e+01
  angle pdb=" C   ASN C  60 "
        pdb=" N   THR C  61 "
        pdb=" CA  THR C  61 "
      ideal   model   delta    sigma   weight residual
     121.54  130.79   -9.25 1.91e+00 2.74e-01 2.34e+01
  angle pdb=" C   ASN A  60 "
        pdb=" N   THR A  61 "
        pdb=" CA  THR A  61 "
      ideal   model   delta    sigma   weight residual
     121.54  130.77   -9.23 1.91e+00 2.74e-01 2.34e+01
  angle pdb=" C   ASN D  60 "
        pdb=" N   THR D  61 "
        pdb=" CA  THR D  61 "
      ideal   model   delta    sigma   weight residual
     121.54  130.75   -9.21 1.91e+00 2.74e-01 2.33e+01
  ... (remaining 17540 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 6751
       17.83 -    35.65: 644
       35.65 -    53.48: 120
       53.48 -    71.31: 10
       71.31 -    89.13: 5
  Dihedral angle restraints: 7530
    sinusoidal: 3025
      harmonic: 4505
  Sorted by residual:
  dihedral pdb=" CA  LEU B 118 "
           pdb=" C   LEU B 118 "
           pdb=" N   PHE B 119 "
           pdb=" CA  PHE B 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.09  -18.91     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  LEU D 118 "
           pdb=" C   LEU D 118 "
           pdb=" N   PHE D 119 "
           pdb=" CA  PHE D 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.09  -18.91     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  LEU A 118 "
           pdb=" C   LEU A 118 "
           pdb=" N   PHE A 119 "
           pdb=" CA  PHE A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.09  -18.91     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 7527 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1293
       0.043 -    0.087: 396
       0.087 -    0.130: 186
       0.130 -    0.174: 59
       0.174 -    0.217: 16
  Chirality restraints: 1950
  Sorted by residual:
  chirality pdb=" CB  ILE A  39 "
            pdb=" CA  ILE A  39 "
            pdb=" CG1 ILE A  39 "
            pdb=" CG2 ILE A  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CB  ILE D  39 "
            pdb=" CA  ILE D  39 "
            pdb=" CG1 ILE D  39 "
            pdb=" CG2 ILE D  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CB  ILE E  39 "
            pdb=" CA  ILE E  39 "
            pdb=" CG1 ILE E  39 "
            pdb=" CG2 ILE E  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 1947 not shown)

  Planarity restraints: 2235
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP D 176 "    0.012 2.00e-02 2.50e+03   2.34e-02 5.47e+00
        pdb=" CG  ASP D 176 "   -0.040 2.00e-02 2.50e+03
        pdb=" OD1 ASP D 176 "    0.015 2.00e-02 2.50e+03
        pdb=" OD2 ASP D 176 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 176 "   -0.011 2.00e-02 2.50e+03   2.33e-02 5.43e+00
        pdb=" CG  ASP A 176 "    0.040 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 176 "   -0.015 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 176 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B 176 "   -0.011 2.00e-02 2.50e+03   2.33e-02 5.43e+00
        pdb=" CG  ASP B 176 "    0.040 2.00e-02 2.50e+03
        pdb=" OD1 ASP B 176 "   -0.015 2.00e-02 2.50e+03
        pdb=" OD2 ASP B 176 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 2232 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 4129
        2.85 -     3.36: 10943
        3.36 -     3.87: 21234
        3.87 -     4.39: 24673
        4.39 -     4.90: 42404
  Nonbonded interactions: 103383
  Sorted by model distance:
  nonbonded pdb=" O   SER C 221 "
            pdb=" OG  SER C 221 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" O   SER B 221 "
            pdb=" OG  SER B 221 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" O   SER E 221 "
            pdb=" OG  SER E 221 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" O   SER D 221 "
            pdb=" OG  SER D 221 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" O   SER A 221 "
            pdb=" OG  SER A 221 "
     model   vdw
     2.335 3.040
  ... (remaining 103378 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             1.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.590
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     28.880
  Find NCS groups from input model:        0.480
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  12880  Z= 0.293
  Angle     :  0.770   9.307  17545  Z= 0.417
  Chirality :  0.056   0.217   1950
  Planarity :  0.005   0.046   2235
  Dihedral  : 14.077  89.134   4620
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.75 (0.22), residues: 1525
  helix:  0.24 (0.23), residues: 500
  sheet:  1.44 (0.25), residues: 460
  loop : -3.01 (0.24), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 206 
 HIS   0.002   0.001   HIS C 177 
 PHE   0.028   0.002   PHE C 116 
 TYR   0.022   0.002   TYR D 248 
 ARG   0.002   0.000   ARG D 299 

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 1.417 
Fit side-chains
REVERT: B  176 ASP cc_start: 0.7075 (t0) cc_final: 0.6855 (t0)
REVERT: A  158 ASP cc_start: 0.6033 (p0) cc_final: 0.5282 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.2689
  time to fit residues: 62.2008
Evaluate side-chains
  145 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    2.9990
   chunk 113 optimal weight:    3.9990
   chunk 63 optimal weight:    0.4980
   chunk 38 optimal weight:    0.5980
   chunk 76 optimal weight:   10.0000
   chunk 60 optimal weight:    6.9990
   chunk 117 optimal weight:    7.9990
   chunk 45 optimal weight:    6.9990
   chunk 71 optimal weight:    6.9990
   chunk 87 optimal weight:    4.9990
   chunk 136 optimal weight:    9.9990
   overall best weight:    2.6186

-------------------------------------------------------------------------------
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: 0.7753
moved from start:          0.1054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12880  Z= 0.267
  Angle     :  0.619   8.718  17545  Z= 0.315
  Chirality :  0.047   0.136   1950
  Planarity :  0.004   0.035   2235
  Dihedral  :  4.997  49.777   1690
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  6.76 %
    Favored  : 93.09 %
  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: -0.35 (0.23), residues: 1525
  helix:  0.91 (0.24), residues: 505
  sheet:  1.68 (0.27), residues: 430
  loop : -2.93 (0.24), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 206 
 HIS   0.003   0.001   HIS A 284 
 PHE   0.020   0.002   PHE C 116 
 TYR   0.019   0.002   TYR C 248 
 ARG   0.002   0.000   ARG E 117 

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 153
  time to evaluate  : 1.530 
Fit side-chains
REVERT: D  176 ASP cc_start: 0.7240 (t0) cc_final: 0.6956 (t0)
REVERT: C  115 ASP cc_start: 0.7145 (t70) cc_final: 0.6628 (t70)
REVERT: A  238 LEU cc_start: 0.8009 (mt) cc_final: 0.7787 (mt)
  outliers start: 2
  outliers final: 1
  residues processed: 154
  average time/residue: 0.2253
  time to fit residues: 52.9012
Evaluate side-chains
  128 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 1.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 42 optimal weight:    0.7980
   chunk 113 optimal weight:    7.9990
   chunk 92 optimal weight:    0.9980
   chunk 37 optimal weight:    6.9990
   chunk 136 optimal weight:    4.9990
   chunk 147 optimal weight:   10.0000
   chunk 121 optimal weight:    6.9990
   chunk 135 optimal weight:    7.9990
   chunk 46 optimal weight:    7.9990
   chunk 109 optimal weight:    5.9990
   overall best weight:    3.9586

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

Flipped N/Q/H residues before XYZ refinement:
E 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.1558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  12880  Z= 0.367
  Angle     :  0.673   9.808  17545  Z= 0.344
  Chirality :  0.050   0.173   1950
  Planarity :  0.004   0.035   2235
  Dihedral  :  5.297  49.461   1690
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 13.60 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.23), residues: 1525
  helix:  0.88 (0.24), residues: 505
  sheet:  1.44 (0.27), residues: 430
  loop : -2.95 (0.24), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 206 
 HIS   0.003   0.001   HIS E 284 
 PHE   0.018   0.002   PHE C 116 
 TYR   0.023   0.002   TYR C 248 
 ARG   0.003   0.001   ARG E 286 

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 1.422 
Fit side-chains
REVERT: E  161 TRP cc_start: 0.7485 (m-10) cc_final: 0.7256 (m-10)
REVERT: E  163 ARG cc_start: 0.6987 (mmt180) cc_final: 0.6780 (mmt180)
REVERT: E  238 LEU cc_start: 0.8044 (mt) cc_final: 0.7812 (mt)
REVERT: D  230 GLU cc_start: 0.5218 (mt-10) cc_final: 0.4595 (mm-30)
REVERT: B  265 MET cc_start: 0.8087 (ttm) cc_final: 0.7876 (ttt)
REVERT: A  151 ASN cc_start: 0.7920 (m110) cc_final: 0.7597 (m-40)
REVERT: A  238 LEU cc_start: 0.8034 (mt) cc_final: 0.7809 (mt)
  outliers start: 16
  outliers final: 13
  residues processed: 156
  average time/residue: 0.2524
  time to fit residues: 57.4930
Evaluate side-chains
  155 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 142
  time to evaluate  : 1.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   54 LYS
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  150 GLU
Chi-restraints excluded: chain D residue  277 ILE
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  150 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 134 optimal weight:    8.9990
   chunk 102 optimal weight:    6.9990
   chunk 70 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 91 optimal weight:    6.9990
   chunk 136 optimal weight:   10.0000
   chunk 144 optimal weight:    0.0000
   chunk 71 optimal weight:    1.9990
   chunk 129 optimal weight:    4.9990
   chunk 39 optimal weight:    6.9990
   overall best weight:    2.3992

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

Flipped N/Q/H residues before XYZ refinement:
E 151 ASN
C 151 ASN
B 151 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12880  Z= 0.245
  Angle     :  0.579   8.756  17545  Z= 0.296
  Chirality :  0.047   0.137   1950
  Planarity :  0.003   0.035   2235
  Dihedral  :  4.939  44.120   1690
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 16.15 %
    Favored  : 82.18 %
  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: -0.34 (0.23), residues: 1525
  helix:  1.06 (0.24), residues: 510
  sheet:  1.37 (0.26), residues: 430
  loop : -2.81 (0.24), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D 206 
 HIS   0.003   0.001   HIS D 284 
 PHE   0.015   0.001   PHE B 116 
 TYR   0.017   0.002   TYR A 248 
 ARG   0.001   0.000   ARG C 299 

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 153
  time to evaluate  : 1.537 
Fit side-chains
REVERT: E   31 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7402 (mp10)
REVERT: D  151 ASN cc_start: 0.7789 (m110) cc_final: 0.7481 (m-40)
REVERT: B  163 ARG cc_start: 0.6928 (mmt180) cc_final: 0.6721 (mmt180)
REVERT: A   31 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7153 (mt0)
REVERT: A  115 ASP cc_start: 0.7231 (t0) cc_final: 0.6832 (t70)
REVERT: A  151 ASN cc_start: 0.7905 (m110) cc_final: 0.7575 (m-40)
  outliers start: 23
  outliers final: 14
  residues processed: 172
  average time/residue: 0.2421
  time to fit residues: 61.4062
Evaluate side-chains
  158 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 142
  time to evaluate  : 1.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   31 GLN
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   54 LYS
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  150 GLU
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  234 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 120 optimal weight:   10.0000
   chunk 82 optimal weight:    6.9990
   chunk 2 optimal weight:    5.9990
   chunk 107 optimal weight:    0.0060
   chunk 59 optimal weight:    7.9990
   chunk 123 optimal weight:    3.9990
   chunk 100 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 74 optimal weight:    9.9990
   chunk 130 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    4.0004

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

Flipped N/Q/H residues before XYZ refinement:
E 151 ASN
E 284 HIS
D 284 HIS
C 151 ASN
C 233 GLN
C 284 HIS
B 284 HIS
A 284 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  12880  Z= 0.368
  Angle     :  0.668   9.813  17545  Z= 0.343
  Chirality :  0.050   0.172   1950
  Planarity :  0.004   0.036   2235
  Dihedral  :  5.343  49.609   1690
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 18.47 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.57 (0.23), residues: 1525
  helix:  0.93 (0.24), residues: 505
  sheet:  1.20 (0.26), residues: 430
  loop : -2.93 (0.24), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D 206 
 HIS   0.003   0.001   HIS A 284 
 PHE   0.016   0.002   PHE B 116 
 TYR   0.021   0.002   TYR A 248 
 ARG   0.003   0.001   ARG C 299 

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 151
  time to evaluate  : 1.462 
Fit side-chains
REVERT: E   31 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7356 (mt0)
REVERT: D   31 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.6698 (mt0)
REVERT: D  151 ASN cc_start: 0.7820 (m110) cc_final: 0.7500 (m-40)
REVERT: D  230 GLU cc_start: 0.5122 (mt-10) cc_final: 0.4451 (mm-30)
REVERT: C   31 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7092 (mt0)
REVERT: B  163 ARG cc_start: 0.6881 (mmt180) cc_final: 0.6633 (mmt180)
REVERT: A   31 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7186 (mt0)
REVERT: A  163 ARG cc_start: 0.6952 (mmt180) cc_final: 0.6739 (mmt180)
  outliers start: 29
  outliers final: 23
  residues processed: 173
  average time/residue: 0.2746
  time to fit residues: 67.0455
Evaluate side-chains
  173 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 146
  time to evaluate  : 1.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   31 GLN
Chi-restraints excluded: chain E residue   39 ILE
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain D residue   31 GLN
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   54 LYS
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  150 GLU
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain D residue  277 ILE
Chi-restraints excluded: chain C residue   31 GLN
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue  168 THR
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  234 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 130 optimal weight:    0.9990
   chunk 28 optimal weight:    0.3980
   chunk 85 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 145 optimal weight:    4.9990
   chunk 120 optimal weight:    3.9990
   chunk 67 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   chunk 76 optimal weight:    6.9990
   chunk 139 optimal weight:    0.9990
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
E 151 ASN
C 151 ASN
C 284 HIS
A 284 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12880  Z= 0.149
  Angle     :  0.515   7.364  17545  Z= 0.263
  Chirality :  0.045   0.128   1950
  Planarity :  0.003   0.036   2235
  Dihedral  :  4.546  34.205   1690
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 19.49 %
    Favored  : 78.84 %
  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: -0.17 (0.23), residues: 1525
  helix:  1.23 (0.24), residues: 515
  sheet:  1.31 (0.26), residues: 435
  loop : -2.67 (0.25), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 206 
 HIS   0.002   0.001   HIS E 284 
 PHE   0.012   0.001   PHE C 116 
 TYR   0.011   0.001   TYR D 248 
 ARG   0.003   0.000   ARG C 231 

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 158
  time to evaluate  : 1.469 
Fit side-chains
REVERT: D  117 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6228 (mpt180)
REVERT: D  151 ASN cc_start: 0.7745 (m110) cc_final: 0.7420 (m-40)
REVERT: C   49 LYS cc_start: 0.7008 (tppt) cc_final: 0.6116 (tptt)
REVERT: C  163 ARG cc_start: 0.6907 (mmt180) cc_final: 0.6674 (mmt180)
REVERT: B   49 LYS cc_start: 0.7006 (tppt) cc_final: 0.6223 (tptt)
REVERT: B  117 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.5295 (mtt180)
REVERT: B  163 ARG cc_start: 0.6848 (mmt180) cc_final: 0.6640 (mmt180)
REVERT: A  117 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6184 (mpt180)
REVERT: A  163 ARG cc_start: 0.6920 (mmt180) cc_final: 0.6718 (mmt180)
  outliers start: 23
  outliers final: 14
  residues processed: 174
  average time/residue: 0.2772
  time to fit residues: 68.0643
Evaluate side-chains
  166 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 149
  time to evaluate  : 1.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain E residue  168 THR
Chi-restraints excluded: chain D residue   54 LYS
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  117 ARG
Chi-restraints excluded: chain D residue  150 GLU
Chi-restraints excluded: chain D residue  168 THR
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  117 ARG
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  117 ARG
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  168 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 82 optimal weight:   10.0000
   chunk 105 optimal weight:    9.9990
   chunk 122 optimal weight:    9.9990
   chunk 81 optimal weight:    0.0670
   chunk 144 optimal weight:    5.9990
   chunk 90 optimal weight:   10.0000
   chunk 88 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 89 optimal weight:   10.0000
   chunk 57 optimal weight:    9.9990
   overall best weight:    3.6126

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

Flipped N/Q/H residues before XYZ refinement:
E 151 ASN
C 151 ASN
C 284 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  12880  Z= 0.333
  Angle     :  0.643   9.471  17545  Z= 0.330
  Chirality :  0.049   0.164   1950
  Planarity :  0.004   0.036   2235
  Dihedral  :  5.096  39.476   1690
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 18.55 %
    Favored  : 78.04 %
  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: -0.39 (0.23), residues: 1525
  helix:  1.11 (0.24), residues: 505
  sheet:  1.25 (0.26), residues: 430
  loop : -2.81 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D 206 
 HIS   0.003   0.001   HIS C 284 
 PHE   0.016   0.002   PHE E 116 
 TYR   0.018   0.002   TYR E 248 
 ARG   0.002   0.000   ARG B  65 

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 152
  time to evaluate  : 1.499 
Fit side-chains
REVERT: E   31 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7343 (mt0)
REVERT: E  163 ARG cc_start: 0.6891 (mmt180) cc_final: 0.6599 (mmt180)
REVERT: D   31 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.6670 (mt0)
REVERT: D  117 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.5753 (mtt180)
REVERT: D  151 ASN cc_start: 0.7836 (m110) cc_final: 0.7500 (m-40)
REVERT: C   31 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7108 (mt0)
REVERT: C   49 LYS cc_start: 0.6995 (tppt) cc_final: 0.6109 (tptt)
REVERT: C  117 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.5633 (mtt180)
REVERT: B   49 LYS cc_start: 0.6996 (tppt) cc_final: 0.6143 (tptt)
REVERT: B  117 ARG cc_start: 0.6959 (OUTLIER) cc_final: 0.5668 (mtt180)
REVERT: B  163 ARG cc_start: 0.6834 (mmt180) cc_final: 0.6611 (mmt180)
REVERT: A   31 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7222 (mt0)
REVERT: A  117 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.5702 (mtt180)
REVERT: A  163 ARG cc_start: 0.6921 (mmt180) cc_final: 0.6714 (mmt180)
  outliers start: 47
  outliers final: 27
  residues processed: 191
  average time/residue: 0.2844
  time to fit residues: 76.3208
Evaluate side-chains
  183 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 148
  time to evaluate  : 1.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   31 GLN
Chi-restraints excluded: chain E residue   39 ILE
Chi-restraints excluded: chain E residue   81 VAL
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain D residue   31 GLN
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   54 LYS
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue  117 ARG
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  150 GLU
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain C residue   31 GLN
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  117 ARG
Chi-restraints excluded: chain C residue  168 THR
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  316 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  117 ARG
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  117 ARG
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  191 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 86 optimal weight:    7.9990
   chunk 43 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 91 optimal weight:    7.9990
   chunk 98 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 113 optimal weight:    0.0770
   chunk 131 optimal weight:    5.9990
   chunk 138 optimal weight:    0.6980
   chunk 126 optimal weight:    0.6980
   overall best weight:    1.0942

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

Flipped N/Q/H residues before XYZ refinement:
E 151 ASN
E 284 HIS
C 151 ASN
C 284 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  12880  Z= 0.162
  Angle     :  0.528   7.218  17545  Z= 0.268
  Chirality :  0.045   0.129   1950
  Planarity :  0.003   0.037   2235
  Dihedral  :  4.495  29.320   1690
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 19.71 %
    Favored  : 78.25 %
  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: -0.09 (0.23), residues: 1525
  helix:  1.30 (0.24), residues: 515
  sheet:  1.35 (0.26), residues: 435
  loop : -2.63 (0.25), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP D 206 
 HIS   0.003   0.001   HIS A 284 
 PHE   0.012   0.001   PHE E 116 
 TYR   0.011   0.001   TYR A 248 
 ARG   0.001   0.000   ARG C 105 

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 151
  time to evaluate  : 1.335 
Fit side-chains
REVERT: E  163 ARG cc_start: 0.6856 (mmt180) cc_final: 0.6550 (mmt180)
REVERT: E  245 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.5723 (t80)
REVERT: D  117 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.5958 (mpt180)
REVERT: D  151 ASN cc_start: 0.7787 (m110) cc_final: 0.7455 (m-40)
REVERT: D  245 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.5892 (t80)
REVERT: C   49 LYS cc_start: 0.6958 (tppt) cc_final: 0.6086 (tptt)
REVERT: C  117 ARG cc_start: 0.6757 (OUTLIER) cc_final: 0.5904 (mpt180)
REVERT: C  163 ARG cc_start: 0.6842 (mmt180) cc_final: 0.6629 (mmt180)
REVERT: C  245 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.6461 (t80)
REVERT: B  117 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.5305 (mtt180)
REVERT: B  163 ARG cc_start: 0.6813 (mmt180) cc_final: 0.6591 (mmt180)
REVERT: B  245 TYR cc_start: 0.7694 (OUTLIER) cc_final: 0.6511 (t80)
REVERT: A  117 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6119 (mpt180)
REVERT: A  163 ARG cc_start: 0.6921 (mmt180) cc_final: 0.6714 (mmt180)
REVERT: A  245 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.5791 (t80)
  outliers start: 28
  outliers final: 15
  residues processed: 174
  average time/residue: 0.2897
  time to fit residues: 70.5261
Evaluate side-chains
  170 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 146
  time to evaluate  : 1.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  245 TYR
Chi-restraints excluded: chain D residue   54 LYS
Chi-restraints excluded: chain D residue  117 ARG
Chi-restraints excluded: chain D residue  150 GLU
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain D residue  245 TYR
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue  117 ARG
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  117 ARG
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  117 ARG
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  245 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 134 optimal weight:   10.0000
   chunk 138 optimal weight:    8.9990
   chunk 81 optimal weight:   20.0000
   chunk 58 optimal weight:    1.9990
   chunk 105 optimal weight:    8.9990
   chunk 41 optimal weight:    4.9990
   chunk 121 optimal weight:    0.5980
   chunk 127 optimal weight:    1.9990
   chunk 88 optimal weight:    0.2980
   chunk 142 optimal weight:    2.9990
   chunk 86 optimal weight:    6.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
E 151 ASN
C 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.1986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12880  Z= 0.190
  Angle     :  0.544   7.927  17545  Z= 0.277
  Chirality :  0.046   0.133   1950
  Planarity :  0.003   0.036   2235
  Dihedral  :  4.528  30.054   1690
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 20.22 %
    Favored  : 77.89 %
  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: -0.02 (0.23), residues: 1525
  helix:  1.35 (0.24), residues: 515
  sheet:  1.41 (0.26), residues: 435
  loop : -2.60 (0.25), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D 206 
 HIS   0.002   0.001   HIS A 284 
 PHE   0.014   0.001   PHE D 116 
 TYR   0.012   0.001   TYR A 248 
 ARG   0.001   0.000   ARG C 299 

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 149
  time to evaluate  : 1.569 
Fit side-chains
REVERT: E   31 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7428 (mp10)
REVERT: E  163 ARG cc_start: 0.6863 (mmt180) cc_final: 0.6553 (mmt180)
REVERT: D  117 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.5326 (mtt180)
REVERT: D  151 ASN cc_start: 0.7827 (m110) cc_final: 0.7477 (m-40)
REVERT: C  117 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.5210 (mtt180)
REVERT: C  163 ARG cc_start: 0.6840 (mmt180) cc_final: 0.6621 (mmt180)
REVERT: C  245 TYR cc_start: 0.7683 (OUTLIER) cc_final: 0.6497 (t80)
REVERT: B  117 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.5445 (mtt180)
REVERT: B  163 ARG cc_start: 0.6800 (mmt180) cc_final: 0.6578 (mmt180)
REVERT: B  233 GLN cc_start: 0.7246 (tp40) cc_final: 0.6814 (mt0)
REVERT: B  245 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.6507 (t80)
REVERT: A  117 ARG cc_start: 0.6948 (OUTLIER) cc_final: 0.6150 (mpt180)
REVERT: A  245 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.5796 (t80)
  outliers start: 26
  outliers final: 14
  residues processed: 170
  average time/residue: 0.2908
  time to fit residues: 68.6456
Evaluate side-chains
  163 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 141
  time to evaluate  : 1.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   31 GLN
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain D residue   54 LYS
Chi-restraints excluded: chain D residue  117 ARG
Chi-restraints excluded: chain D residue  150 GLU
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain C residue  117 ARG
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  117 ARG
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue  117 ARG
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  245 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   chunk 149 optimal weight:    8.9990
   chunk 137 optimal weight:    6.9990
   chunk 118 optimal weight:    8.9990
   chunk 12 optimal weight:    0.6980
   chunk 91 optimal weight:    6.9990
   chunk 72 optimal weight:    0.1980
   chunk 94 optimal weight:    8.9990
   chunk 126 optimal weight:    4.9990
   chunk 36 optimal weight:    0.6980
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
E 151 ASN
C 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.2013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12880  Z= 0.199
  Angle     :  0.552   7.886  17545  Z= 0.281
  Chirality :  0.046   0.142   1950
  Planarity :  0.003   0.036   2235
  Dihedral  :  4.554  29.808   1690
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 20.00 %
    Favored  : 77.89 %
  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:  0.01 (0.23), residues: 1525
  helix:  1.36 (0.24), residues: 515
  sheet:  1.43 (0.26), residues: 435
  loop : -2.56 (0.25), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP D 206 
 HIS   0.003   0.001   HIS A 284 
 PHE   0.016   0.001   PHE E 116 
 TYR   0.014   0.001   TYR A 248 
 ARG   0.001   0.000   ARG C 299 

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 143
  time to evaluate  : 1.501 
Fit side-chains
REVERT: E   31 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7431 (mp10)
REVERT: E  163 ARG cc_start: 0.6872 (mmt180) cc_final: 0.6550 (mmt180)
REVERT: D  117 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.5287 (mtt180)
REVERT: D  151 ASN cc_start: 0.7806 (m110) cc_final: 0.7458 (m-40)
REVERT: C   49 LYS cc_start: 0.6973 (tppt) cc_final: 0.6183 (tptt)
REVERT: C  117 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.5229 (mtt180)
REVERT: C  245 TYR cc_start: 0.7689 (OUTLIER) cc_final: 0.6516 (t80)
REVERT: B  117 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.5327 (mtt180)
REVERT: B  163 ARG cc_start: 0.6805 (mmt180) cc_final: 0.6581 (mmt180)
REVERT: B  233 GLN cc_start: 0.7259 (tp40) cc_final: 0.6828 (mt0)
REVERT: B  245 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.6552 (t80)
REVERT: A  117 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6202 (mpt180)
REVERT: A  245 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.5802 (t80)
  outliers start: 29
  outliers final: 17
  residues processed: 166
  average time/residue: 0.3067
  time to fit residues: 71.3893
Evaluate side-chains
  167 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 142
  time to evaluate  : 1.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   31 GLN
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain D residue   54 LYS
Chi-restraints excluded: chain D residue  117 ARG
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  150 GLU
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue  117 ARG
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  117 ARG
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue  117 ARG
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  245 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 109 optimal weight:    6.9990
   chunk 17 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 119 optimal weight:    0.6980
   chunk 49 optimal weight:    7.9990
   chunk 122 optimal weight:    9.9990
   chunk 15 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9990
   chunk 104 optimal weight:    7.9990
   chunk 6 optimal weight:    6.9990
   chunk 86 optimal weight:    5.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
E 151 ASN
C 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.148376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.115913 restraints weight = 13919.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 1.55
r_work: 0.3065 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  12880  Z= 0.303
  Angle     :  0.625   8.956  17545  Z= 0.318
  Chirality :  0.048   0.168   1950
  Planarity :  0.003   0.036   2235
  Dihedral  :  4.901  34.096   1690
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 19.64 %
    Favored  : 77.89 %
  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: -0.18 (0.23), residues: 1525
  helix:  1.19 (0.24), residues: 515
  sheet:  1.28 (0.26), residues: 435
  loop : -2.61 (0.25), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP D 206 
 HIS   0.003   0.001   HIS B 284 
 PHE   0.015   0.002   PHE B 116 
 TYR   0.018   0.002   TYR A 248 
 ARG   0.002   0.000   ARG B  65 
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 2671.87 seconds
wall clock time: 49 minutes 8.09 seconds (2948.09 seconds total)