Starting phenix.real_space_refine
on Wed Mar  4 12:39:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dlu_30713/03_2026/7dlu_30713.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dlu_30713/03_2026/7dlu_30713.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dlu_30713/03_2026/7dlu_30713.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dlu_30713/03_2026/7dlu_30713.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dlu_30713/03_2026/7dlu_30713.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dlu_30713/03_2026/7dlu_30713.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=  -0.005 sd=   0.171
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      28      5.16       5
     C    8911      2.51       5
     N    2345      2.21       5
     O    2443      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 91 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13727
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 260, 1961
          Classifications: {'peptide': 260}
          Link IDs: {'PTRANS': 9, 'TRANS': 250}
  Restraints were copied for chains:
    B, C, D, E, F, G
  Time building chain proxies: 1.71, per 1000 atoms: 0.12
  Number of scatterers: 13727
  At special positions: 0
  Unit cell: (101.091, 100.004, 141.31, 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      28     16.00
     O    2443      8.00
     N    2345      7.00
     C    8911      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: 0.82
  Conformation dependent library (CDL) restraints added in 519.2 milliseconds
  

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3290

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 16 sheets defined
      54.2% alpha, 22.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 54
      removed outlier: 3.701A  pdb=" N   VAL A  19 " --> pdb=" O   TRP A  15 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LYS A  25 " --> pdb=" O   GLU A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 85
      removed outlier: 3.510A  pdb=" N   GLY A  62 " --> pdb=" O   ARG A  58 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   PHE A  63 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   VAL A  64 " --> pdb=" O   LEU A  60 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU A  67 " --> pdb=" O   PHE A  63 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLY A  85 " --> pdb=" O   ALA A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 105
    Processing helix  chain 'A' and resid 106 through 122
    Processing helix  chain 'A' and resid 162 through 167
    Processing helix  chain 'A' and resid 192 through 202
    Processing helix  chain 'A' and resid 239 through 256
      removed outlier: 4.752A  pdb=" N   ARG A 252 " --> pdb=" O   ASN A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 259
      No H-bonds generated for 'chain 'A' and resid 257 through 259'
    Processing helix  chain 'B' and resid 15 through 54
      removed outlier: 3.701A  pdb=" N   VAL B  19 " --> pdb=" O   TRP B  15 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LYS B  25 " --> pdb=" O   GLU B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 85
      removed outlier: 3.510A  pdb=" N   GLY B  62 " --> pdb=" O   ARG B  58 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   PHE B  63 " --> pdb=" O   THR B  59 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   VAL B  64 " --> pdb=" O   LEU B  60 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU B  67 " --> pdb=" O   PHE B  63 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLY B  85 " --> pdb=" O   ALA B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 105
    Processing helix  chain 'B' and resid 106 through 122
    Processing helix  chain 'B' and resid 162 through 167
    Processing helix  chain 'B' and resid 192 through 202
    Processing helix  chain 'B' and resid 239 through 256
      removed outlier: 4.751A  pdb=" N   ARG B 252 " --> pdb=" O   ASN B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 259
      No H-bonds generated for 'chain 'B' and resid 257 through 259'
    Processing helix  chain 'C' and resid 15 through 54
      removed outlier: 3.701A  pdb=" N   VAL C  19 " --> pdb=" O   TRP C  15 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LYS C  25 " --> pdb=" O   GLU C  21 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 58 through 85
      removed outlier: 3.511A  pdb=" N   GLY C  62 " --> pdb=" O   ARG C  58 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   PHE C  63 " --> pdb=" O   THR C  59 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   VAL C  64 " --> pdb=" O   LEU C  60 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LEU C  67 " --> pdb=" O   PHE C  63 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLY C  85 " --> pdb=" O   ALA C  81 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 88 through 105
    Processing helix  chain 'C' and resid 106 through 122
    Processing helix  chain 'C' and resid 162 through 167
    Processing helix  chain 'C' and resid 192 through 202
    Processing helix  chain 'C' and resid 239 through 256
      removed outlier: 4.752A  pdb=" N   ARG C 252 " --> pdb=" O   ASN C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 257 through 259
      No H-bonds generated for 'chain 'C' and resid 257 through 259'
    Processing helix  chain 'D' and resid 15 through 54
      removed outlier: 3.701A  pdb=" N   VAL D  19 " --> pdb=" O   TRP D  15 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LYS D  25 " --> pdb=" O   GLU D  21 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 85
      removed outlier: 3.511A  pdb=" N   GLY D  62 " --> pdb=" O   ARG D  58 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   PHE D  63 " --> pdb=" O   THR D  59 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   VAL D  64 " --> pdb=" O   LEU D  60 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU D  67 " --> pdb=" O   PHE D  63 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLY D  85 " --> pdb=" O   ALA D  81 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 88 through 105
    Processing helix  chain 'D' and resid 106 through 122
    Processing helix  chain 'D' and resid 162 through 167
    Processing helix  chain 'D' and resid 192 through 202
    Processing helix  chain 'D' and resid 239 through 256
      removed outlier: 4.751A  pdb=" N   ARG D 252 " --> pdb=" O   ASN D 248 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 257 through 259
      No H-bonds generated for 'chain 'D' and resid 257 through 259'
    Processing helix  chain 'E' and resid 15 through 54
      removed outlier: 3.701A  pdb=" N   VAL E  19 " --> pdb=" O   TRP E  15 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LYS E  25 " --> pdb=" O   GLU E  21 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 58 through 85
      removed outlier: 3.511A  pdb=" N   GLY E  62 " --> pdb=" O   ARG E  58 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   PHE E  63 " --> pdb=" O   THR E  59 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   VAL E  64 " --> pdb=" O   LEU E  60 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU E  67 " --> pdb=" O   PHE E  63 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLY E  85 " --> pdb=" O   ALA E  81 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 88 through 105
    Processing helix  chain 'E' and resid 106 through 122
    Processing helix  chain 'E' and resid 162 through 167
    Processing helix  chain 'E' and resid 192 through 202
    Processing helix  chain 'E' and resid 239 through 256
      removed outlier: 4.752A  pdb=" N   ARG E 252 " --> pdb=" O   ASN E 248 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 257 through 259
      No H-bonds generated for 'chain 'E' and resid 257 through 259'
    Processing helix  chain 'F' and resid 15 through 54
      removed outlier: 3.701A  pdb=" N   VAL F  19 " --> pdb=" O   TRP F  15 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LYS F  25 " --> pdb=" O   GLU F  21 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 58 through 85
      removed outlier: 3.510A  pdb=" N   GLY F  62 " --> pdb=" O   ARG F  58 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   PHE F  63 " --> pdb=" O   THR F  59 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   VAL F  64 " --> pdb=" O   LEU F  60 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU F  67 " --> pdb=" O   PHE F  63 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLY F  85 " --> pdb=" O   ALA F  81 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 88 through 105
    Processing helix  chain 'F' and resid 106 through 122
    Processing helix  chain 'F' and resid 162 through 167
    Processing helix  chain 'F' and resid 192 through 202
    Processing helix  chain 'F' and resid 239 through 256
      removed outlier: 4.752A  pdb=" N   ARG F 252 " --> pdb=" O   ASN F 248 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 257 through 259
      No H-bonds generated for 'chain 'F' and resid 257 through 259'
    Processing helix  chain 'G' and resid 15 through 54
      removed outlier: 3.701A  pdb=" N   VAL G  19 " --> pdb=" O   TRP G  15 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LYS G  25 " --> pdb=" O   GLU G  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 58 through 85
      removed outlier: 3.511A  pdb=" N   GLY G  62 " --> pdb=" O   ARG G  58 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   PHE G  63 " --> pdb=" O   THR G  59 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   VAL G  64 " --> pdb=" O   LEU G  60 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU G  67 " --> pdb=" O   PHE G  63 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLY G  85 " --> pdb=" O   ALA G  81 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 88 through 105
    Processing helix  chain 'G' and resid 106 through 122
    Processing helix  chain 'G' and resid 162 through 167
    Processing helix  chain 'G' and resid 192 through 202
    Processing helix  chain 'G' and resid 239 through 256
      removed outlier: 4.752A  pdb=" N   ARG G 252 " --> pdb=" O   ASN G 248 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 257 through 259
      No H-bonds generated for 'chain 'G' and resid 257 through 259'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 130 through 133
      removed outlier: 6.798A  pdb=" N   VAL A 149 " --> pdb=" O   ASP A 141 " (cutoff:3.500A)
      removed outlier: 5.293A  pdb=" N   ILE A 143 " --> pdb=" O   HIS A 147 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   HIS A 147 " --> pdb=" O   ILE A 143 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   VAL B 149 " --> pdb=" O   ASP B 141 " (cutoff:3.500A)
      removed outlier: 5.293A  pdb=" N   ILE B 143 " --> pdb=" O   HIS B 147 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   HIS B 147 " --> pdb=" O   ILE B 143 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   VAL C 149 " --> pdb=" O   ASP C 141 " (cutoff:3.500A)
      removed outlier: 5.292A  pdb=" N   ILE C 143 " --> pdb=" O   HIS C 147 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   HIS C 147 " --> pdb=" O   ILE C 143 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   VAL D 149 " --> pdb=" O   ASP D 141 " (cutoff:3.500A)
      removed outlier: 5.292A  pdb=" N   ILE D 143 " --> pdb=" O   HIS D 147 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   HIS D 147 " --> pdb=" O   ILE D 143 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   VAL E 149 " --> pdb=" O   ASP E 141 " (cutoff:3.500A)
      removed outlier: 5.293A  pdb=" N   ILE E 143 " --> pdb=" O   HIS E 147 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   HIS E 147 " --> pdb=" O   ILE E 143 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   VAL F 149 " --> pdb=" O   ASP F 141 " (cutoff:3.500A)
      removed outlier: 5.293A  pdb=" N   ILE F 143 " --> pdb=" O   HIS F 147 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   HIS F 147 " --> pdb=" O   ILE F 143 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   VAL G 149 " --> pdb=" O   ASP G 141 " (cutoff:3.500A)
      removed outlier: 5.293A  pdb=" N   ILE G 143 " --> pdb=" O   HIS G 147 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   HIS G 147 " --> pdb=" O   ILE G 143 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181
    Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 181
      removed outlier: 4.614A  pdb=" N   THR A 228 " --> pdb=" O   SER A 220 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 266 through 272
      removed outlier: 6.827A  pdb=" N   ARG A 267 " --> pdb=" O   LYS B 270 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   VAL B 272 " --> pdb=" O   ARG A 267 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   VAL A 269 " --> pdb=" O   VAL B 272 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   ARG B 267 " --> pdb=" O   LYS C 270 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   VAL C 272 " --> pdb=" O   ARG B 267 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   VAL B 269 " --> pdb=" O   VAL C 272 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   ARG C 267 " --> pdb=" O   LYS D 270 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   VAL D 272 " --> pdb=" O   ARG C 267 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   VAL C 269 " --> pdb=" O   VAL D 272 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   ARG D 267 " --> pdb=" O   LYS E 270 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   VAL E 272 " --> pdb=" O   ARG D 267 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   VAL D 269 " --> pdb=" O   VAL E 272 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   ARG E 267 " --> pdb=" O   LYS F 270 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   VAL F 272 " --> pdb=" O   ARG E 267 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   VAL E 269 " --> pdb=" O   VAL F 272 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   ARG F 267 " --> pdb=" O   LYS G 270 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   VAL G 272 " --> pdb=" O   ARG F 267 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   VAL F 269 " --> pdb=" O   VAL G 272 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 178 through 181
    Processing sheet with id=AA6, first strand: chain 'B' and resid 178 through 181
      removed outlier: 4.614A  pdb=" N   THR B 228 " --> pdb=" O   SER B 220 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 178 through 181
    Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 181
      removed outlier: 4.613A  pdb=" N   THR C 228 " --> pdb=" O   SER C 220 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 178 through 181
    Processing sheet with id=AB1, first strand: chain 'D' and resid 178 through 181
      removed outlier: 4.614A  pdb=" N   THR D 228 " --> pdb=" O   SER D 220 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 178 through 181
    Processing sheet with id=AB3, first strand: chain 'E' and resid 178 through 181
      removed outlier: 4.614A  pdb=" N   THR E 228 " --> pdb=" O   SER E 220 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 178 through 181
    Processing sheet with id=AB5, first strand: chain 'F' and resid 178 through 181
      removed outlier: 4.613A  pdb=" N   THR F 228 " --> pdb=" O   SER F 220 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'G' and resid 178 through 181
    Processing sheet with id=AB7, first strand: chain 'G' and resid 178 through 181
      removed outlier: 4.614A  pdb=" N   THR G 228 " --> pdb=" O   SER G 220 " (cutoff:3.500A)

    957 hydrogen bonds defined for protein.
    2745 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.30

  Time building geometry restraints manager: 1.10 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: 4422
        1.34 -     1.46: 1847
        1.46 -     1.57: 7647
        1.57 -     1.69: 0
        1.69 -     1.80: 56
  Bond restraints: 13972
  Sorted by residual:
  bond pdb=" C   GLU F 249 "
       pdb=" O   GLU F 249 "
    ideal  model  delta    sigma   weight residual
    1.235  1.252 -0.017 1.10e-02 8.26e+03 2.42e+00
  bond pdb=" C   GLU B 249 "
       pdb=" O   GLU B 249 "
    ideal  model  delta    sigma   weight residual
    1.235  1.252 -0.017 1.10e-02 8.26e+03 2.41e+00
  bond pdb=" C   GLU E 249 "
       pdb=" O   GLU E 249 "
    ideal  model  delta    sigma   weight residual
    1.235  1.252 -0.017 1.10e-02 8.26e+03 2.38e+00
  bond pdb=" C   GLU D 249 "
       pdb=" O   GLU D 249 "
    ideal  model  delta    sigma   weight residual
    1.235  1.252 -0.017 1.10e-02 8.26e+03 2.38e+00
  bond pdb=" C   GLU A 249 "
       pdb=" O   GLU A 249 "
    ideal  model  delta    sigma   weight residual
    1.235  1.252 -0.017 1.10e-02 8.26e+03 2.38e+00
  ... (remaining 13967 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 18594
        1.90 -     3.80: 327
        3.80 -     5.70: 84
        5.70 -     7.60: 14
        7.60 -     9.50: 14
  Bond angle restraints: 19033
  Sorted by residual:
  angle pdb=" C   VAL C 181 "
        pdb=" N   ILE C 182 "
        pdb=" CA  ILE C 182 "
      ideal   model   delta    sigma   weight residual
     121.97  112.47    9.50 1.80e+00 3.09e-01 2.79e+01
  angle pdb=" C   VAL F 181 "
        pdb=" N   ILE F 182 "
        pdb=" CA  ILE F 182 "
      ideal   model   delta    sigma   weight residual
     121.97  112.47    9.50 1.80e+00 3.09e-01 2.79e+01
  angle pdb=" C   VAL E 181 "
        pdb=" N   ILE E 182 "
        pdb=" CA  ILE E 182 "
      ideal   model   delta    sigma   weight residual
     121.97  112.48    9.49 1.80e+00 3.09e-01 2.78e+01
  angle pdb=" C   VAL G 181 "
        pdb=" N   ILE G 182 "
        pdb=" CA  ILE G 182 "
      ideal   model   delta    sigma   weight residual
     121.97  112.48    9.49 1.80e+00 3.09e-01 2.78e+01
  angle pdb=" C   VAL A 181 "
        pdb=" N   ILE A 182 "
        pdb=" CA  ILE A 182 "
      ideal   model   delta    sigma   weight residual
     121.97  112.48    9.49 1.80e+00 3.09e-01 2.78e+01
  ... (remaining 19028 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.72: 6732
       11.72 -    23.45: 920
       23.45 -    35.17: 342
       35.17 -    46.90: 161
       46.90 -    58.62: 70
  Dihedral angle restraints: 8225
    sinusoidal: 3094
      harmonic: 5131
  Sorted by residual:
  dihedral pdb=" CA  ASP G 212 "
           pdb=" C   ASP G 212 "
           pdb=" N   PRO G 213 "
           pdb=" CA  PRO G 213 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.88   23.12     0      5.00e+00 4.00e-02 2.14e+01
  dihedral pdb=" CA  ASP E 212 "
           pdb=" C   ASP E 212 "
           pdb=" N   PRO E 213 "
           pdb=" CA  PRO E 213 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.89   23.11     0      5.00e+00 4.00e-02 2.14e+01
  dihedral pdb=" CA  ASP F 212 "
           pdb=" C   ASP F 212 "
           pdb=" N   PRO F 213 "
           pdb=" CA  PRO F 213 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.90   23.10     0      5.00e+00 4.00e-02 2.14e+01
  ... (remaining 8222 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1284
       0.031 -    0.063: 651
       0.063 -    0.094: 231
       0.094 -    0.125: 137
       0.125 -    0.156: 21
  Chirality restraints: 2324
  Sorted by residual:
  chirality pdb=" CA  VAL G 181 "
            pdb=" N   VAL G 181 "
            pdb=" C   VAL G 181 "
            pdb=" CB  VAL G 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.10e-01
  chirality pdb=" CA  VAL C 181 "
            pdb=" N   VAL C 181 "
            pdb=" C   VAL C 181 "
            pdb=" CB  VAL C 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.03e-01
  chirality pdb=" CA  VAL B 181 "
            pdb=" N   VAL B 181 "
            pdb=" C   VAL B 181 "
            pdb=" CB  VAL B 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.15 2.00e-01 2.50e+01 6.00e-01
  ... (remaining 2321 not shown)

  Planarity restraints: 2380
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 264 "   -0.048 5.00e-02 4.00e+02   7.22e-02 8.35e+00
        pdb=" N   PRO B 265 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO B 265 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B 265 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE E 264 "   -0.048 5.00e-02 4.00e+02   7.22e-02 8.35e+00
        pdb=" N   PRO E 265 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO E 265 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO E 265 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 264 "   -0.048 5.00e-02 4.00e+02   7.22e-02 8.34e+00
        pdb=" N   PRO C 265 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO C 265 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO C 265 "   -0.040 5.00e-02 4.00e+02
  ... (remaining 2377 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.28: 14
        2.28 -     2.94: 5922
        2.94 -     3.59: 19242
        3.59 -     4.25: 30076
        4.25 -     4.90: 52046
  Nonbonded interactions: 107300
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 154 "
            pdb=" NH2 ARG B 179 "
     model   vdw
     1.627 3.120
  nonbonded pdb=" OD2 ASP C 154 "
            pdb=" NH2 ARG D 179 "
     model   vdw
     1.627 3.120
  nonbonded pdb=" OD2 ASP E 154 "
            pdb=" NH2 ARG F 179 "
     model   vdw
     1.627 3.120
  nonbonded pdb=" OD2 ASP B 154 "
            pdb=" NH2 ARG C 179 "
     model   vdw
     1.627 3.120
  nonbonded pdb=" NH2 ARG A 179 "
            pdb=" OD2 ASP G 154 "
     model   vdw
     1.627 3.120
  ... (remaining 107295 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

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:             1.140
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     11.170
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  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:6.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
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      :  0.004   0.024  13972  Z= 0.199
  Angle     :  0.717   9.502  19033  Z= 0.409
  Chirality :  0.047   0.156   2324
  Planarity :  0.005   0.072   2380
  Dihedral  : 15.055  58.623   4935
  Min Nonbonded Distance : 1.627

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.78 %
    Allowed  :  6.59 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  6.73 %
    Allowed  : 16.35 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.19), residues: 1806
  helix:  0.20 (0.16), residues: 938
  sheet: -2.35 (0.26), residues: 273
  loop : -1.67 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E  58 
 TYR   0.005   0.001   TYR E 173 
 PHE   0.021   0.002   PHE E  63 
 TRP   0.007   0.001   TRP C 130 
 HIS   0.001   0.000   HIS D 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (13972)
  covalent geometry    : angle       0.71715 (19033)
  hydrogen bonds       : bond        0.10700 (  929)
  hydrogen bonds       : angle       4.39802 ( 2745)

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

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

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 98
    poor density    : 217
  time to evaluate  : 0.457 
Fit side-chains
REVERT: A   46 ARG cc_start: 0.6345 (ttm170) cc_final: 0.5881 (ttt90)
REVERT: A   87 GLN cc_start: 0.8645 (mm110) cc_final: 0.8092 (mm-40)
REVERT: A  145 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7616 (pp)
REVERT: B   46 ARG cc_start: 0.6089 (ttm170) cc_final: 0.5405 (ttt90)
REVERT: B  145 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7594 (pp)
REVERT: B  270 LYS cc_start: 0.8943 (tttt) cc_final: 0.8722 (tttt)
REVERT: C   46 ARG cc_start: 0.6610 (ttm170) cc_final: 0.5959 (ttt90)
REVERT: C   51 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7148 (mp)
REVERT: C  145 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7436 (pp)
REVERT: C  180 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8410 (ttt180)
REVERT: C  270 LYS cc_start: 0.8921 (tttt) cc_final: 0.8672 (tttm)
REVERT: D   46 ARG cc_start: 0.6415 (ttm170) cc_final: 0.5716 (ttt-90)
REVERT: D   95 ILE cc_start: 0.8017 (mp) cc_final: 0.7678 (mt)
REVERT: D  126 LYS cc_start: 0.8831 (ptpp) cc_final: 0.8567 (pttt)
REVERT: D  145 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7563 (pp)
REVERT: E   46 ARG cc_start: 0.6440 (ttm170) cc_final: 0.5685 (ttt90)
REVERT: E   51 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7014 (mp)
REVERT: E  145 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7341 (pp)
REVERT: F   46 ARG cc_start: 0.6336 (ttm170) cc_final: 0.5661 (ttt90)
REVERT: F   54 ARG cc_start: 0.7137 (mtp180) cc_final: 0.6829 (mtt-85)
REVERT: F   87 GLN cc_start: 0.8736 (mm110) cc_final: 0.8268 (mm-40)
REVERT: F  126 LYS cc_start: 0.8770 (ptpp) cc_final: 0.8541 (pttt)
REVERT: F  141 ASP cc_start: 0.8054 (t0) cc_final: 0.7816 (t70)
REVERT: F  145 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7423 (pp)
REVERT: G   46 ARG cc_start: 0.6425 (ttm170) cc_final: 0.5765 (ttt-90)
REVERT: G   51 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7337 (mp)
REVERT: G  145 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7511 (pp)
REVERT: G  270 LYS cc_start: 0.8883 (tttt) cc_final: 0.8461 (tttp)
  outliers start: 98
  outliers final: 53
  residues processed: 306
  average time/residue: 0.6261
  time to fit residues: 207.2075
Evaluate side-chains
  253 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 189
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  180 ARG
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  273 GLN
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  221 ASN
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  273 GLN
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   57 ASP
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  109 SER
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  152 SER
Chi-restraints excluded: chain C residue  180 ARG
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  221 ASN
Chi-restraints excluded: chain C residue  272 VAL
Chi-restraints excluded: chain C residue  273 GLN
Chi-restraints excluded: chain D residue   57 ASP
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  152 SER
Chi-restraints excluded: chain D residue  216 VAL
Chi-restraints excluded: chain D residue  221 ASN
Chi-restraints excluded: chain D residue  272 VAL
Chi-restraints excluded: chain D residue  273 GLN
Chi-restraints excluded: chain E residue   51 LEU
Chi-restraints excluded: chain E residue   57 ASP
Chi-restraints excluded: chain E residue  109 SER
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  152 SER
Chi-restraints excluded: chain E residue  180 ARG
Chi-restraints excluded: chain E residue  216 VAL
Chi-restraints excluded: chain E residue  221 ASN
Chi-restraints excluded: chain E residue  272 VAL
Chi-restraints excluded: chain E residue  273 GLN
Chi-restraints excluded: chain F residue   57 ASP
Chi-restraints excluded: chain F residue  109 SER
Chi-restraints excluded: chain F residue  145 ILE
Chi-restraints excluded: chain F residue  216 VAL
Chi-restraints excluded: chain F residue  221 ASN
Chi-restraints excluded: chain F residue  272 VAL
Chi-restraints excluded: chain F residue  273 GLN
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain G residue   57 ASP
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue  109 SER
Chi-restraints excluded: chain G residue  145 ILE
Chi-restraints excluded: chain G residue  180 ARG
Chi-restraints excluded: chain G residue  216 VAL
Chi-restraints excluded: chain G residue  272 VAL
Chi-restraints excluded: chain G residue  273 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:   30.0000
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    0.0870
   overall best weight:    1.2164

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

Flipped N/Q/H residues before XYZ refinement:
A  61 GLN
A  87 GLN
A 147 HIS
A 155 ASN
A 248 ASN
B  61 GLN
B 147 HIS
B 155 ASN
B 248 ASN
C  61 GLN
C 147 HIS
C 155 ASN
C 248 ASN
D  61 GLN
D 147 HIS
D 155 ASN
D 248 ASN
E  61 GLN
E 147 HIS
E 155 ASN
E 197 GLN
E 248 ASN
F  61 GLN
F  87 GLN
F 147 HIS
F 155 ASN
F 248 ASN
G  61 GLN
G 147 HIS
G 155 ASN
G 248 ASN

Total number of N/Q/H flips: 31

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.131190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.095307 restraints weight = 15715.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 1.83
r_work: 0.2971 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2847 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.1225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13972  Z= 0.154
  Angle     :  0.661   9.395  19033  Z= 0.356
  Chirality :  0.045   0.141   2324
  Planarity :  0.005   0.070   2380
  Dihedral  :  8.581  59.930   2045
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.78 %
    Allowed  :  6.20 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 21.09 %
    Favored  : 75.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.20), residues: 1806
  helix:  1.27 (0.17), residues: 945
  sheet: -1.87 (0.27), residues: 273
  loop : -1.12 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  58 
 TYR   0.009   0.001   TYR E 173 
 PHE   0.014   0.001   PHE C  63 
 TRP   0.005   0.001   TRP E  15 
 HIS   0.002   0.001   HIS C 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (13972)
  covalent geometry    : angle       0.66115 (19033)
  hydrogen bonds       : bond        0.05718 (  929)
  hydrogen bonds       : angle       3.95708 ( 2745)

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

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

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 222
  time to evaluate  : 0.478 
Fit side-chains
REVERT: A   46 ARG cc_start: 0.6372 (ttm170) cc_final: 0.5718 (ttt90)
REVERT: A   87 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8185 (mm-40)
REVERT: A  145 ILE cc_start: 0.8070 (mt) cc_final: 0.7698 (pp)
REVERT: A  232 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8176 (mtt-85)
REVERT: B   46 ARG cc_start: 0.6028 (ttm170) cc_final: 0.5221 (ttt90)
REVERT: B  145 ILE cc_start: 0.8026 (mt) cc_final: 0.7673 (pp)
REVERT: B  206 ASP cc_start: 0.8509 (t70) cc_final: 0.8295 (t0)
REVERT: B  232 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8121 (mtt-85)
REVERT: B  270 LYS cc_start: 0.8825 (tttt) cc_final: 0.8607 (tttt)
REVERT: C   46 ARG cc_start: 0.6532 (ttm170) cc_final: 0.5706 (ttt90)
REVERT: C  145 ILE cc_start: 0.8054 (mt) cc_final: 0.7547 (pp)
REVERT: C  232 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8203 (mtt-85)
REVERT: C  270 LYS cc_start: 0.8788 (tttt) cc_final: 0.8365 (tttp)
REVERT: D   46 ARG cc_start: 0.6286 (ttm170) cc_final: 0.5511 (ttt-90)
REVERT: D   51 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7381 (mp)
REVERT: D   95 ILE cc_start: 0.8035 (mp) cc_final: 0.7662 (mt)
REVERT: D  145 ILE cc_start: 0.8118 (mt) cc_final: 0.7655 (pp)
REVERT: D  154 ASP cc_start: 0.7828 (t70) cc_final: 0.7503 (t0)
REVERT: D  232 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8160 (mtt-85)
REVERT: E   46 ARG cc_start: 0.6190 (ttm170) cc_final: 0.5380 (ttt90)
REVERT: E  145 ILE cc_start: 0.8115 (mt) cc_final: 0.7641 (pp)
REVERT: E  154 ASP cc_start: 0.7668 (t70) cc_final: 0.7402 (t0)
REVERT: E  232 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8119 (mtt-85)
REVERT: F   46 ARG cc_start: 0.6320 (ttm170) cc_final: 0.5903 (mtp-110)
REVERT: F   51 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.6982 (mp)
REVERT: F   87 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8296 (mm-40)
REVERT: F   95 ILE cc_start: 0.8011 (mp) cc_final: 0.7791 (mt)
REVERT: F  141 ASP cc_start: 0.8765 (t0) cc_final: 0.8542 (t70)
REVERT: F  145 ILE cc_start: 0.7858 (mt) cc_final: 0.7524 (pp)
REVERT: F  154 ASP cc_start: 0.7806 (t70) cc_final: 0.7443 (t0)
REVERT: F  232 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8168 (mtt-85)
REVERT: G   46 ARG cc_start: 0.6361 (ttm170) cc_final: 0.5625 (ttt-90)
REVERT: G   95 ILE cc_start: 0.7993 (mp) cc_final: 0.7769 (mt)
REVERT: G  145 ILE cc_start: 0.8059 (mt) cc_final: 0.7610 (pp)
REVERT: G  232 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8622 (mtt-85)
REVERT: G  270 LYS cc_start: 0.8801 (tttt) cc_final: 0.8328 (tttp)
  outliers start: 47
  outliers final: 24
  residues processed: 260
  average time/residue: 0.6526
  time to fit residues: 183.0620
Evaluate side-chains
  235 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 202
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  180 ARG
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  232 ARG
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain B residue  192 ASP
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  232 ARG
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  126 LYS
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  232 ARG
Chi-restraints excluded: chain C residue  272 VAL
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue  216 VAL
Chi-restraints excluded: chain D residue  232 ARG
Chi-restraints excluded: chain D residue  272 VAL
Chi-restraints excluded: chain E residue   87 GLN
Chi-restraints excluded: chain E residue  180 ARG
Chi-restraints excluded: chain E residue  216 VAL
Chi-restraints excluded: chain E residue  232 ARG
Chi-restraints excluded: chain E residue  272 VAL
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue  216 VAL
Chi-restraints excluded: chain F residue  232 ARG
Chi-restraints excluded: chain F residue  272 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue  180 ARG
Chi-restraints excluded: chain G residue  216 VAL
Chi-restraints excluded: chain G residue  232 ARG
Chi-restraints excluded: chain G residue  272 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 134 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 128 optimal weight:    4.9990
   chunk 46 optimal weight:    0.2980
   chunk 20 optimal weight:    3.9990
   chunk 159 optimal weight:    0.7980
   chunk 104 optimal weight:   20.0000
   chunk 176 optimal weight:    4.9990
   chunk 169 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 197 GLN
D 197 GLN
F 197 GLN
G  41 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.134143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.098594 restraints weight = 15887.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 1.83
r_work: 0.3024 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13972  Z= 0.126
  Angle     :  0.596   8.384  19033  Z= 0.318
  Chirality :  0.044   0.142   2324
  Planarity :  0.005   0.066   2380
  Dihedral  :  6.459  57.912   1961
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.78 %
    Allowed  :  5.32 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 22.12 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.21), residues: 1806
  helix:  1.87 (0.17), residues: 938
  sheet: -1.59 (0.28), residues: 273
  loop : -0.87 (0.27), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 123 
 TYR   0.007   0.001   TYR E 173 
 PHE   0.012   0.001   PHE E  63 
 TRP   0.005   0.001   TRP C 241 
 HIS   0.002   0.001   HIS F 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (13972)
  covalent geometry    : angle       0.59567 (19033)
  hydrogen bonds       : bond        0.04864 (  929)
  hydrogen bonds       : angle       3.79465 ( 2745)

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

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

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 218
  time to evaluate  : 0.490 
Fit side-chains
REVERT: A   46 ARG cc_start: 0.6393 (ttm170) cc_final: 0.5740 (ttt90)
REVERT: A   87 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8163 (mm-40)
REVERT: A  145 ILE cc_start: 0.7946 (mt) cc_final: 0.7637 (pp)
REVERT: A  184 ASP cc_start: 0.7628 (m-30) cc_final: 0.7425 (m-30)
REVERT: A  232 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7747 (mtt-85)
REVERT: B   46 ARG cc_start: 0.6055 (ttm170) cc_final: 0.5261 (ttt90)
REVERT: B  145 ILE cc_start: 0.7946 (mt) cc_final: 0.7647 (pp)
REVERT: B  154 ASP cc_start: 0.7511 (t70) cc_final: 0.7256 (t70)
REVERT: B  232 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.7678 (mtt-85)
REVERT: B  270 LYS cc_start: 0.8833 (tttt) cc_final: 0.8611 (tttt)
REVERT: C   46 ARG cc_start: 0.6564 (ttm170) cc_final: 0.5740 (ttt90)
REVERT: C   87 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8232 (mm-40)
REVERT: C  145 ILE cc_start: 0.8084 (mt) cc_final: 0.7510 (pp)
REVERT: C  232 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.7766 (mtt-85)
REVERT: C  270 LYS cc_start: 0.8838 (tttt) cc_final: 0.8419 (tttp)
REVERT: D   46 ARG cc_start: 0.6331 (ttm170) cc_final: 0.5479 (ttp80)
REVERT: D   95 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7711 (mt)
REVERT: D  123 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7813 (mtt90)
REVERT: D  145 ILE cc_start: 0.8033 (mt) cc_final: 0.7660 (pp)
REVERT: D  216 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8689 (m)
REVERT: D  232 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.7807 (mtt-85)
REVERT: E   46 ARG cc_start: 0.6239 (ttm170) cc_final: 0.5446 (ttp80)
REVERT: E  145 ILE cc_start: 0.8019 (mt) cc_final: 0.7581 (pp)
REVERT: E  154 ASP cc_start: 0.7661 (t70) cc_final: 0.7433 (t70)
REVERT: E  216 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8658 (m)
REVERT: E  232 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8490 (mtt90)
REVERT: F   51 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.6999 (mp)
REVERT: F   87 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8209 (mm-40)
REVERT: F   95 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7897 (mt)
REVERT: F  145 ILE cc_start: 0.7909 (mt) cc_final: 0.7589 (pp)
REVERT: F  154 ASP cc_start: 0.7712 (t70) cc_final: 0.7445 (t70)
REVERT: F  232 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.7871 (mtt-85)
REVERT: G   46 ARG cc_start: 0.6366 (ttm170) cc_final: 0.5660 (ttt-90)
REVERT: G   95 ILE cc_start: 0.7988 (mp) cc_final: 0.7751 (mt)
REVERT: G  145 ILE cc_start: 0.7960 (mt) cc_final: 0.7544 (pp)
REVERT: G  154 ASP cc_start: 0.7516 (t70) cc_final: 0.7265 (t70)
REVERT: G  206 ASP cc_start: 0.8199 (t70) cc_final: 0.7987 (t70)
REVERT: G  270 LYS cc_start: 0.8822 (tttt) cc_final: 0.8349 (tttp)
  outliers start: 49
  outliers final: 20
  residues processed: 253
  average time/residue: 0.6449
  time to fit residues: 176.4042
Evaluate side-chains
  255 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 223
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 ARG
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  232 ARG
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  232 ARG
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  232 ARG
Chi-restraints excluded: chain C residue  272 VAL
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   95 ILE
Chi-restraints excluded: chain D residue  123 ARG
Chi-restraints excluded: chain D residue  216 VAL
Chi-restraints excluded: chain D residue  232 ARG
Chi-restraints excluded: chain D residue  272 VAL
Chi-restraints excluded: chain E residue  192 ASP
Chi-restraints excluded: chain E residue  216 VAL
Chi-restraints excluded: chain E residue  232 ARG
Chi-restraints excluded: chain E residue  272 VAL
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue   95 ILE
Chi-restraints excluded: chain F residue  216 VAL
Chi-restraints excluded: chain F residue  232 ARG
Chi-restraints excluded: chain F residue  272 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue  180 ARG
Chi-restraints excluded: chain G residue  192 ASP
Chi-restraints excluded: chain G residue  216 VAL
Chi-restraints excluded: chain G residue  272 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 116 optimal weight:    5.9990
   chunk 59 optimal weight:    0.6980
   chunk 153 optimal weight:    1.9990
   chunk 2 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 174 optimal weight:    0.7980
   chunk 108 optimal weight:    5.9990
   chunk 30 optimal weight:    0.2980
   chunk 64 optimal weight:    4.9990
   chunk 85 optimal weight:    0.7980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
E 195 ASN
F 195 ASN
G  41 ASN
G 195 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.133287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.098689 restraints weight = 15823.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 1.76
r_work: 0.3024 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2900 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13972  Z= 0.130
  Angle     :  0.597   8.449  19033  Z= 0.319
  Chirality :  0.044   0.143   2324
  Planarity :  0.005   0.065   2380
  Dihedral  :  5.962  57.941   1956
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.78 %
    Allowed  :  6.09 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 22.73 %
    Favored  : 74.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.21), residues: 1806
  helix:  2.05 (0.17), residues: 945
  sheet: -1.28 (0.29), residues: 266
  loop : -0.70 (0.27), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  46 
 TYR   0.008   0.001   TYR E 173 
 PHE   0.013   0.001   PHE E  63 
 TRP   0.005   0.001   TRP C 241 
 HIS   0.002   0.001   HIS F 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (13972)
  covalent geometry    : angle       0.59659 (19033)
  hydrogen bonds       : bond        0.04951 (  929)
  hydrogen bonds       : angle       3.73770 ( 2745)

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

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

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 228
  time to evaluate  : 0.523 
Fit side-chains
REVERT: A   46 ARG cc_start: 0.6391 (ttm170) cc_final: 0.5742 (ttt90)
REVERT: A   87 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8186 (mm-40)
REVERT: A  145 ILE cc_start: 0.7964 (mt) cc_final: 0.7673 (pp)
REVERT: A  232 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.7784 (mtt-85)
REVERT: B   46 ARG cc_start: 0.6030 (ttm170) cc_final: 0.5237 (ttt90)
REVERT: B  145 ILE cc_start: 0.7984 (mt) cc_final: 0.7723 (pp)
REVERT: B  232 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7668 (mtt-85)
REVERT: B  250 LYS cc_start: 0.6886 (mtmt) cc_final: 0.6651 (mtmm)
REVERT: B  270 LYS cc_start: 0.8854 (tttt) cc_final: 0.8632 (tttt)
REVERT: C   46 ARG cc_start: 0.6626 (ttm170) cc_final: 0.5825 (ttt90)
REVERT: C   87 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8263 (mm-40)
REVERT: C  145 ILE cc_start: 0.8089 (mt) cc_final: 0.7824 (tp)
REVERT: C  192 ASP cc_start: 0.7859 (t0) cc_final: 0.7645 (t0)
REVERT: C  232 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.7766 (mtt-85)
REVERT: C  270 LYS cc_start: 0.8841 (tttt) cc_final: 0.8438 (tttp)
REVERT: D   46 ARG cc_start: 0.6330 (ttm170) cc_final: 0.5483 (ttp80)
REVERT: D   95 ILE cc_start: 0.8061 (mp) cc_final: 0.7716 (mt)
REVERT: D  123 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7805 (mtt90)
REVERT: D  145 ILE cc_start: 0.7991 (mt) cc_final: 0.7726 (pp)
REVERT: D  206 ASP cc_start: 0.8354 (t70) cc_final: 0.8058 (t70)
REVERT: D  232 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7833 (mtt-85)
REVERT: E   46 ARG cc_start: 0.6232 (ttm170) cc_final: 0.5423 (ttp80)
REVERT: E  145 ILE cc_start: 0.8015 (mt) cc_final: 0.7580 (pp)
REVERT: E  154 ASP cc_start: 0.7640 (t70) cc_final: 0.7417 (t70)
REVERT: E  206 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.8095 (t70)
REVERT: F   46 ARG cc_start: 0.6589 (ttm110) cc_final: 0.6297 (mtp-110)
REVERT: F   51 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.6932 (mp)
REVERT: F   87 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8239 (mm-40)
REVERT: F   95 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7899 (mt)
REVERT: F  145 ILE cc_start: 0.7916 (mt) cc_final: 0.7594 (pp)
REVERT: F  154 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7514 (t70)
REVERT: F  206 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.8035 (t70)
REVERT: F  216 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8682 (m)
REVERT: F  232 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.7818 (mtt-85)
REVERT: G   46 ARG cc_start: 0.6400 (ttm170) cc_final: 0.5695 (ttt-90)
REVERT: G   95 ILE cc_start: 0.8067 (mp) cc_final: 0.7836 (mt)
REVERT: G  145 ILE cc_start: 0.7967 (mt) cc_final: 0.7565 (pp)
REVERT: G  154 ASP cc_start: 0.7521 (t70) cc_final: 0.7259 (t70)
REVERT: G  206 ASP cc_start: 0.8185 (t70) cc_final: 0.7943 (t70)
REVERT: G  270 LYS cc_start: 0.8822 (tttt) cc_final: 0.8354 (tttp)
  outliers start: 47
  outliers final: 19
  residues processed: 259
  average time/residue: 0.6117
  time to fit residues: 171.6905
Evaluate side-chains
  234 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 203
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 ARG
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  232 ARG
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  273 GLN
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   90 SER
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  232 ARG
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain C residue  232 ARG
Chi-restraints excluded: chain C residue  272 VAL
Chi-restraints excluded: chain D residue  123 ARG
Chi-restraints excluded: chain D residue  232 ARG
Chi-restraints excluded: chain D residue  272 VAL
Chi-restraints excluded: chain E residue  109 SER
Chi-restraints excluded: chain E residue  206 ASP
Chi-restraints excluded: chain E residue  272 VAL
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue   57 ASP
Chi-restraints excluded: chain F residue   95 ILE
Chi-restraints excluded: chain F residue  154 ASP
Chi-restraints excluded: chain F residue  206 ASP
Chi-restraints excluded: chain F residue  216 VAL
Chi-restraints excluded: chain F residue  232 ARG
Chi-restraints excluded: chain F residue  272 VAL
Chi-restraints excluded: chain G residue   57 ASP
Chi-restraints excluded: chain G residue  109 SER
Chi-restraints excluded: chain G residue  180 ARG
Chi-restraints excluded: chain G residue  272 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 81 optimal weight:    9.9990
   chunk 96 optimal weight:    0.9990
   chunk 179 optimal weight:    0.9990
   chunk 175 optimal weight:    3.9990
   chunk 118 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 172 optimal weight:    0.7980
   chunk 132 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 174 optimal weight:    0.7980
   chunk 134 optimal weight:    2.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
B 195 ASN
E 195 ASN
G  41 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.134444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.098799 restraints weight = 15850.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 1.83
r_work: 0.3024 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2900 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13972  Z= 0.128
  Angle     :  0.594   8.176  19033  Z= 0.318
  Chirality :  0.044   0.155   2324
  Planarity :  0.005   0.065   2380
  Dihedral  :  5.565  58.607   1949
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.78 %
    Allowed  :  5.92 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 23.08 %
    Favored  : 73.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.21), residues: 1806
  helix:  2.13 (0.17), residues: 952
  sheet: -0.77 (0.30), residues: 280
  loop : -0.52 (0.28), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  46 
 TYR   0.008   0.001   TYR E 173 
 PHE   0.013   0.001   PHE G  63 
 TRP   0.006   0.001   TRP C 241 
 HIS   0.002   0.001   HIS F 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (13972)
  covalent geometry    : angle       0.59363 (19033)
  hydrogen bonds       : bond        0.04863 (  929)
  hydrogen bonds       : angle       3.69961 ( 2745)

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

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

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 214
  time to evaluate  : 0.427 
Fit side-chains
REVERT: A   46 ARG cc_start: 0.6359 (ttm170) cc_final: 0.5708 (ttt90)
REVERT: A   87 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8233 (mm-40)
REVERT: A  145 ILE cc_start: 0.8079 (mt) cc_final: 0.7744 (pp)
REVERT: A  184 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6867 (m-30)
REVERT: A  232 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7728 (mtt-85)
REVERT: B   46 ARG cc_start: 0.6037 (ttm170) cc_final: 0.5246 (ttt90)
REVERT: B  145 ILE cc_start: 0.7920 (mt) cc_final: 0.7665 (pp)
REVERT: B  232 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.7571 (mtt-85)
REVERT: B  250 LYS cc_start: 0.6860 (mtmt) cc_final: 0.6621 (mtmm)
REVERT: B  270 LYS cc_start: 0.8815 (tttt) cc_final: 0.8589 (tttt)
REVERT: C   46 ARG cc_start: 0.6574 (ttm170) cc_final: 0.5721 (ttt90)
REVERT: C   87 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8334 (mm-40)
REVERT: C  145 ILE cc_start: 0.8105 (mt) cc_final: 0.7836 (tp)
REVERT: C  194 LYS cc_start: 0.8191 (tppt) cc_final: 0.7805 (tptp)
REVERT: C  232 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.7721 (mtt-85)
REVERT: C  270 LYS cc_start: 0.8801 (tttt) cc_final: 0.8393 (tttp)
REVERT: D   46 ARG cc_start: 0.6302 (ttm170) cc_final: 0.5453 (ttp80)
REVERT: D   51 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7145 (mp)
REVERT: D   95 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7649 (mt)
REVERT: D  123 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7815 (mtt90)
REVERT: D  145 ILE cc_start: 0.7930 (mt) cc_final: 0.7669 (pp)
REVERT: D  154 ASP cc_start: 0.7879 (t70) cc_final: 0.7652 (t0)
REVERT: D  232 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7744 (mtt-85)
REVERT: E   46 ARG cc_start: 0.6212 (ttm170) cc_final: 0.5399 (ttp80)
REVERT: E  145 ILE cc_start: 0.7992 (mt) cc_final: 0.7553 (pp)
REVERT: E  154 ASP cc_start: 0.7535 (t70) cc_final: 0.7332 (t70)
REVERT: E  206 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.8029 (t70)
REVERT: F   51 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6934 (mp)
REVERT: F   87 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8284 (mm-40)
REVERT: F   95 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7840 (mt)
REVERT: F  145 ILE cc_start: 0.7959 (mt) cc_final: 0.7663 (pp)
REVERT: F  154 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7497 (t70)
REVERT: F  206 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7997 (t70)
REVERT: F  232 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.7801 (mtt-85)
REVERT: G   46 ARG cc_start: 0.6335 (ttm170) cc_final: 0.5641 (ttt-90)
REVERT: G   95 ILE cc_start: 0.8047 (mp) cc_final: 0.7803 (mt)
REVERT: G  145 ILE cc_start: 0.8154 (mt) cc_final: 0.7677 (pp)
REVERT: G  154 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7243 (t70)
REVERT: G  206 ASP cc_start: 0.8187 (t70) cc_final: 0.7946 (t70)
REVERT: G  232 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8418 (mtt-85)
REVERT: G  270 LYS cc_start: 0.8773 (tttt) cc_final: 0.8306 (tttp)
  outliers start: 49
  outliers final: 20
  residues processed: 250
  average time/residue: 0.6286
  time to fit residues: 170.1663
Evaluate side-chains
  235 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 199
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  180 ARG
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  232 ARG
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   90 SER
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  232 ARG
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain C residue  109 SER
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  232 ARG
Chi-restraints excluded: chain C residue  272 VAL
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   95 ILE
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  123 ARG
Chi-restraints excluded: chain D residue  232 ARG
Chi-restraints excluded: chain D residue  272 VAL
Chi-restraints excluded: chain E residue  109 SER
Chi-restraints excluded: chain E residue  206 ASP
Chi-restraints excluded: chain E residue  272 VAL
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue   57 ASP
Chi-restraints excluded: chain F residue   95 ILE
Chi-restraints excluded: chain F residue  109 SER
Chi-restraints excluded: chain F residue  154 ASP
Chi-restraints excluded: chain F residue  206 ASP
Chi-restraints excluded: chain F residue  232 ARG
Chi-restraints excluded: chain F residue  272 VAL
Chi-restraints excluded: chain G residue  109 SER
Chi-restraints excluded: chain G residue  154 ASP
Chi-restraints excluded: chain G residue  180 ARG
Chi-restraints excluded: chain G residue  232 ARG
Chi-restraints excluded: chain G residue  272 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 77 optimal weight:    0.1980
   chunk 44 optimal weight:    0.8980
   chunk 21 optimal weight:    7.9990
   chunk 177 optimal weight:    7.9990
   chunk 175 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 152 optimal weight:    1.9990
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
E 195 ASN
G  41 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.130737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.094791 restraints weight = 15741.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 1.82
r_work: 0.2964 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2838 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024  13972  Z= 0.169
  Angle     :  0.646   9.143  19033  Z= 0.349
  Chirality :  0.046   0.181   2324
  Planarity :  0.005   0.067   2380
  Dihedral  :  5.585  59.523   1947
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.78 %
    Allowed  :  6.76 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 23.08 %
    Favored  : 73.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.21), residues: 1806
  helix:  2.11 (0.17), residues: 952
  sheet: -0.78 (0.30), residues: 280
  loop : -0.52 (0.29), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  46 
 TYR   0.011   0.002   TYR E 173 
 PHE   0.017   0.002   PHE C  63 
 TRP   0.006   0.001   TRP C 241 
 HIS   0.002   0.001   HIS F 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (13972)
  covalent geometry    : angle       0.64624 (19033)
  hydrogen bonds       : bond        0.05871 (  929)
  hydrogen bonds       : angle       3.76101 ( 2745)

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

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

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 220
  time to evaluate  : 0.535 
Fit side-chains
REVERT: A   46 ARG cc_start: 0.6366 (ttm170) cc_final: 0.5699 (ttt90)
REVERT: A   51 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7198 (mp)
REVERT: A   87 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8233 (mm-40)
REVERT: A  145 ILE cc_start: 0.8062 (mt) cc_final: 0.7739 (pp)
REVERT: A  184 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6892 (m-30)
REVERT: A  232 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8165 (mtt-85)
REVERT: B   46 ARG cc_start: 0.6127 (ttm170) cc_final: 0.5338 (ttt90)
REVERT: B  145 ILE cc_start: 0.8015 (mt) cc_final: 0.7743 (pp)
REVERT: B  232 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8169 (mtt-85)
REVERT: B  270 LYS cc_start: 0.8790 (tttt) cc_final: 0.8561 (tttt)
REVERT: C   46 ARG cc_start: 0.6599 (ttm170) cc_final: 0.5714 (ttt90)
REVERT: C   87 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8257 (mm-40)
REVERT: C  145 ILE cc_start: 0.8152 (mt) cc_final: 0.7880 (tp)
REVERT: C  194 LYS cc_start: 0.8159 (tppt) cc_final: 0.7778 (tptp)
REVERT: C  270 LYS cc_start: 0.8838 (tttt) cc_final: 0.8418 (tttp)
REVERT: D   46 ARG cc_start: 0.6302 (ttm170) cc_final: 0.5425 (ttp80)
REVERT: D   51 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7096 (mp)
REVERT: D   95 ILE cc_start: 0.7996 (mp) cc_final: 0.7644 (mt)
REVERT: D  123 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7941 (mtt90)
REVERT: D  145 ILE cc_start: 0.8179 (mt) cc_final: 0.7861 (pp)
REVERT: D  154 ASP cc_start: 0.7847 (t70) cc_final: 0.7488 (t0)
REVERT: D  206 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8113 (t70)
REVERT: D  232 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8088 (mtt-85)
REVERT: E   46 ARG cc_start: 0.6226 (ttm170) cc_final: 0.5399 (ttp80)
REVERT: E   51 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6967 (mp)
REVERT: E  145 ILE cc_start: 0.8091 (mt) cc_final: 0.7619 (pp)
REVERT: E  154 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7350 (t70)
REVERT: E  206 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8124 (t70)
REVERT: E  250 LYS cc_start: 0.7641 (mtpm) cc_final: 0.7407 (mtmm)
REVERT: F   46 ARG cc_start: 0.6511 (ttm110) cc_final: 0.6210 (mtp-110)
REVERT: F   51 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.6942 (mp)
REVERT: F   87 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8338 (mm-40)
REVERT: F  145 ILE cc_start: 0.8062 (mt) cc_final: 0.7737 (pp)
REVERT: F  154 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7500 (t70)
REVERT: F  232 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8202 (mtt-85)
REVERT: G   46 ARG cc_start: 0.6371 (ttm170) cc_final: 0.5629 (ttt-90)
REVERT: G   51 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7114 (mp)
REVERT: G   95 ILE cc_start: 0.8016 (mp) cc_final: 0.7794 (mt)
REVERT: G  145 ILE cc_start: 0.8077 (mt) cc_final: 0.7627 (pp)
REVERT: G  154 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7279 (t70)
REVERT: G  206 ASP cc_start: 0.8247 (t70) cc_final: 0.7977 (t70)
REVERT: G  270 LYS cc_start: 0.8776 (tttt) cc_final: 0.8293 (tttp)
  outliers start: 44
  outliers final: 19
  residues processed: 255
  average time/residue: 0.6533
  time to fit residues: 179.8959
Evaluate side-chains
  254 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 219
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  180 ARG
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  232 ARG
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  232 ARG
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain C residue  109 SER
Chi-restraints excluded: chain C residue  272 VAL
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  123 ARG
Chi-restraints excluded: chain D residue  206 ASP
Chi-restraints excluded: chain D residue  232 ARG
Chi-restraints excluded: chain D residue  272 VAL
Chi-restraints excluded: chain E residue   51 LEU
Chi-restraints excluded: chain E residue  109 SER
Chi-restraints excluded: chain E residue  154 ASP
Chi-restraints excluded: chain E residue  206 ASP
Chi-restraints excluded: chain E residue  272 VAL
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue  109 SER
Chi-restraints excluded: chain F residue  154 ASP
Chi-restraints excluded: chain F residue  232 ARG
Chi-restraints excluded: chain F residue  272 VAL
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain G residue   57 ASP
Chi-restraints excluded: chain G residue  109 SER
Chi-restraints excluded: chain G residue  154 ASP
Chi-restraints excluded: chain G residue  180 ARG
Chi-restraints excluded: chain G residue  272 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 124 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9990
   chunk 88 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 162 optimal weight:    0.8980
   chunk 171 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 139 optimal weight:    3.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
E 195 ASN
G  41 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.132409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.096363 restraints weight = 15680.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3105 rms_B_bonded: 1.84
r_work: 0.2985 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2859 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13972  Z= 0.143
  Angle     :  0.615   8.554  19033  Z= 0.332
  Chirality :  0.045   0.164   2324
  Planarity :  0.005   0.067   2380
  Dihedral  :  5.538  59.895   1947
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.78 %
    Allowed  :  6.53 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 22.94 %
    Favored  : 73.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.21), residues: 1806
  helix:  2.21 (0.17), residues: 952
  sheet: -0.71 (0.30), residues: 280
  loop : -0.45 (0.29), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  46 
 TYR   0.009   0.001   TYR E 173 
 PHE   0.014   0.002   PHE D  63 
 TRP   0.006   0.001   TRP C 241 
 HIS   0.002   0.001   HIS F 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (13972)
  covalent geometry    : angle       0.61546 (19033)
  hydrogen bonds       : bond        0.05309 (  929)
  hydrogen bonds       : angle       3.72201 ( 2745)

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

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

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 220
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A   46 ARG cc_start: 0.6338 (ttm170) cc_final: 0.5669 (ttt90)
REVERT: A   87 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8248 (mm-40)
REVERT: A  145 ILE cc_start: 0.8003 (mt) cc_final: 0.7689 (pp)
REVERT: A  184 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6978 (m-30)
REVERT: A  232 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.7955 (mtt-85)
REVERT: B   46 ARG cc_start: 0.6102 (ttm170) cc_final: 0.5315 (ttt90)
REVERT: B  145 ILE cc_start: 0.7980 (mt) cc_final: 0.7689 (pp)
REVERT: B  232 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.7921 (mtt-85)
REVERT: B  270 LYS cc_start: 0.8765 (tttt) cc_final: 0.8538 (tttt)
REVERT: C   46 ARG cc_start: 0.6556 (ttm170) cc_final: 0.5672 (ttt90)
REVERT: C   51 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6847 (mp)
REVERT: C   87 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8293 (mm-40)
REVERT: C  145 ILE cc_start: 0.8146 (mt) cc_final: 0.7910 (tp)
REVERT: C  154 ASP cc_start: 0.7776 (t0) cc_final: 0.7405 (t0)
REVERT: C  192 ASP cc_start: 0.8083 (t0) cc_final: 0.7870 (t0)
REVERT: C  194 LYS cc_start: 0.8100 (tppt) cc_final: 0.7724 (tptp)
REVERT: C  232 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8023 (mtt-85)
REVERT: C  270 LYS cc_start: 0.8807 (tttt) cc_final: 0.8379 (tttp)
REVERT: D   46 ARG cc_start: 0.6261 (ttm170) cc_final: 0.5387 (ttp80)
REVERT: D   51 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7053 (mp)
REVERT: D   95 ILE cc_start: 0.8005 (mp) cc_final: 0.7661 (mt)
REVERT: D  123 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7893 (mtt90)
REVERT: D  145 ILE cc_start: 0.8173 (mt) cc_final: 0.7839 (pp)
REVERT: D  154 ASP cc_start: 0.7915 (t70) cc_final: 0.7552 (t0)
REVERT: D  232 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8007 (mtt-85)
REVERT: E   46 ARG cc_start: 0.6188 (ttm170) cc_final: 0.5364 (ttp80)
REVERT: E   51 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6950 (mp)
REVERT: E  145 ILE cc_start: 0.7987 (mt) cc_final: 0.7536 (pp)
REVERT: E  154 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7313 (t70)
REVERT: E  206 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.8053 (t70)
REVERT: E  250 LYS cc_start: 0.7439 (mtpm) cc_final: 0.7209 (mtmm)
REVERT: F   46 ARG cc_start: 0.6402 (ttm110) cc_final: 0.5542 (ttt180)
REVERT: F   51 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6950 (mp)
REVERT: F   87 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8248 (mm-40)
REVERT: F  145 ILE cc_start: 0.8029 (mt) cc_final: 0.7700 (pp)
REVERT: F  154 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7502 (t70)
REVERT: F  232 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8076 (mtt-85)
REVERT: G   46 ARG cc_start: 0.6352 (ttm170) cc_final: 0.5611 (ttt-90)
REVERT: G   51 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7116 (mp)
REVERT: G   95 ILE cc_start: 0.7978 (mp) cc_final: 0.7757 (mt)
REVERT: G  145 ILE cc_start: 0.8077 (mt) cc_final: 0.7640 (pp)
REVERT: G  154 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7233 (t70)
REVERT: G  206 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7790 (t70)
REVERT: G  270 LYS cc_start: 0.8757 (tttt) cc_final: 0.8279 (tttp)
  outliers start: 51
  outliers final: 20
  residues processed: 262
  average time/residue: 0.6256
  time to fit residues: 177.2783
Evaluate side-chains
  242 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 205
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  180 ARG
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  232 ARG
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   90 SER
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  232 ARG
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  109 SER
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  232 ARG
Chi-restraints excluded: chain C residue  272 VAL
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  123 ARG
Chi-restraints excluded: chain D residue  232 ARG
Chi-restraints excluded: chain D residue  272 VAL
Chi-restraints excluded: chain E residue   51 LEU
Chi-restraints excluded: chain E residue  109 SER
Chi-restraints excluded: chain E residue  154 ASP
Chi-restraints excluded: chain E residue  206 ASP
Chi-restraints excluded: chain E residue  272 VAL
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue  109 SER
Chi-restraints excluded: chain F residue  154 ASP
Chi-restraints excluded: chain F residue  232 ARG
Chi-restraints excluded: chain F residue  272 VAL
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain G residue  109 SER
Chi-restraints excluded: chain G residue  154 ASP
Chi-restraints excluded: chain G residue  180 ARG
Chi-restraints excluded: chain G residue  206 ASP
Chi-restraints excluded: chain G residue  272 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 69 optimal weight:    0.0870
   chunk 44 optimal weight:    3.9990
   chunk 129 optimal weight:    0.7980
   chunk 63 optimal weight:    0.0570
   chunk 134 optimal weight:    0.8980
   chunk 105 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 164 optimal weight:    4.9990
   chunk 150 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 132 optimal weight:    7.9990
   overall best weight:    0.4676

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

Flipped N/Q/H residues before XYZ refinement:
B 197 GLN
D 197 GLN
F 197 GLN
G  41 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.138054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.102774 restraints weight = 15719.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 1.82
r_work: 0.3082 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  13972  Z= 0.114
  Angle     :  0.558   7.767  19033  Z= 0.298
  Chirality :  0.044   0.189   2324
  Planarity :  0.005   0.065   2380
  Dihedral  :  5.260  59.246   1947
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.78 %
    Allowed  :  5.43 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 23.21 %
    Favored  : 73.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.56 (0.21), residues: 1806
  helix:  2.38 (0.17), residues: 952
  sheet: -0.56 (0.30), residues: 280
  loop : -0.38 (0.29), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  54 
 TYR   0.005   0.001   TYR C 240 
 PHE   0.009   0.001   PHE D  63 
 TRP   0.006   0.001   TRP E 241 
 HIS   0.002   0.001   HIS F 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (13972)
  covalent geometry    : angle       0.55792 (19033)
  hydrogen bonds       : bond        0.04071 (  929)
  hydrogen bonds       : angle       3.64388 ( 2745)

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

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

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 215
  time to evaluate  : 0.504 
Fit side-chains
REVERT: A   46 ARG cc_start: 0.6429 (ttm170) cc_final: 0.5730 (ttt90)
REVERT: A   87 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8151 (mm-40)
REVERT: A  145 ILE cc_start: 0.7887 (mt) cc_final: 0.7624 (pp)
REVERT: B   46 ARG cc_start: 0.6054 (ttm170) cc_final: 0.5257 (ttt90)
REVERT: B  145 ILE cc_start: 0.7934 (mt) cc_final: 0.7609 (pp)
REVERT: B  232 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7191 (mtt-85)
REVERT: B  270 LYS cc_start: 0.8748 (tttt) cc_final: 0.8516 (tttt)
REVERT: C   46 ARG cc_start: 0.6618 (ttm170) cc_final: 0.5788 (ttt90)
REVERT: C  154 ASP cc_start: 0.7525 (t0) cc_final: 0.7187 (t0)
REVERT: C  194 LYS cc_start: 0.8128 (tppt) cc_final: 0.7778 (tptp)
REVERT: C  270 LYS cc_start: 0.8826 (tttt) cc_final: 0.8412 (tttp)
REVERT: D   46 ARG cc_start: 0.6362 (ttm170) cc_final: 0.5496 (ttp80)
REVERT: D   51 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6958 (mp)
REVERT: D   95 ILE cc_start: 0.7952 (mp) cc_final: 0.7594 (mt)
REVERT: D  154 ASP cc_start: 0.7641 (t70) cc_final: 0.7307 (t0)
REVERT: D  206 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7915 (t70)
REVERT: D  232 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7250 (mtt-85)
REVERT: E   46 ARG cc_start: 0.6222 (ttm170) cc_final: 0.5388 (ttp80)
REVERT: E  184 ASP cc_start: 0.6937 (OUTLIER) cc_final: 0.6687 (m-30)
REVERT: E  206 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7850 (t70)
REVERT: F   46 ARG cc_start: 0.6452 (ttm110) cc_final: 0.5727 (ttp80)
REVERT: F   51 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6915 (mp)
REVERT: F   83 MET cc_start: 0.8352 (ttm) cc_final: 0.8133 (ttp)
REVERT: F   87 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8272 (mm-40)
REVERT: F  154 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7470 (t70)
REVERT: G   46 ARG cc_start: 0.6409 (ttm170) cc_final: 0.5659 (ttt-90)
REVERT: G   95 ILE cc_start: 0.8040 (mp) cc_final: 0.7786 (mt)
REVERT: G  154 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7160 (t70)
REVERT: G  206 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7630 (t70)
REVERT: G  270 LYS cc_start: 0.8815 (tttt) cc_final: 0.8333 (tttp)
  outliers start: 47
  outliers final: 27
  residues processed: 252
  average time/residue: 0.6223
  time to fit residues: 169.8520
Evaluate side-chains
  248 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 211
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  174 SER
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   90 SER
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  232 ARG
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  109 SER
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  272 VAL
Chi-restraints excluded: chain C residue  273 GLN
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   57 ASP
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  206 ASP
Chi-restraints excluded: chain D residue  232 ARG
Chi-restraints excluded: chain D residue  272 VAL
Chi-restraints excluded: chain D residue  273 GLN
Chi-restraints excluded: chain E residue  109 SER
Chi-restraints excluded: chain E residue  184 ASP
Chi-restraints excluded: chain E residue  206 ASP
Chi-restraints excluded: chain E residue  272 VAL
Chi-restraints excluded: chain E residue  273 GLN
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue   57 ASP
Chi-restraints excluded: chain F residue  109 SER
Chi-restraints excluded: chain F residue  154 ASP
Chi-restraints excluded: chain F residue  272 VAL
Chi-restraints excluded: chain G residue   57 ASP
Chi-restraints excluded: chain G residue  109 SER
Chi-restraints excluded: chain G residue  154 ASP
Chi-restraints excluded: chain G residue  206 ASP
Chi-restraints excluded: chain G residue  272 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 130 optimal weight:   30.0000
   chunk 133 optimal weight:    3.9990
   chunk 159 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 119 optimal weight:    0.9980
   chunk 109 optimal weight:    0.9990
   chunk 129 optimal weight:    0.8980
   chunk 174 optimal weight:    2.9990
   chunk 86 optimal weight:    4.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
B 197 GLN
C 197 GLN
F 197 GLN
F 266 GLN
G  41 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.134880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.100450 restraints weight = 15745.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 1.74
r_work: 0.3044 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13972  Z= 0.129
  Angle     :  0.587   8.115  19033  Z= 0.315
  Chirality :  0.044   0.190   2324
  Planarity :  0.005   0.065   2380
  Dihedral  :  4.690  32.370   1939
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.78 %
    Allowed  :  5.98 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 23.70 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.60 (0.21), residues: 1806
  helix:  2.36 (0.17), residues: 959
  sheet: -0.55 (0.30), residues: 280
  loop : -0.31 (0.29), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  54 
 TYR   0.009   0.001   TYR E 173 
 PHE   0.011   0.001   PHE D  63 
 TRP   0.006   0.001   TRP C 241 
 HIS   0.002   0.001   HIS F 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (13972)
  covalent geometry    : angle       0.58681 (19033)
  hydrogen bonds       : bond        0.04684 (  929)
  hydrogen bonds       : angle       3.60617 ( 2745)

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

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

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 217
  time to evaluate  : 0.529 
Fit side-chains
REVERT: A   46 ARG cc_start: 0.6378 (ttm170) cc_final: 0.5705 (ttt90)
REVERT: A   87 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8265 (mm-40)
REVERT: A  145 ILE cc_start: 0.7984 (mt) cc_final: 0.7709 (pp)
REVERT: A  195 ASN cc_start: 0.8600 (t0) cc_final: 0.8164 (t0)
REVERT: B   46 ARG cc_start: 0.6065 (ttm170) cc_final: 0.5276 (ttt90)
REVERT: B  145 ILE cc_start: 0.7983 (mt) cc_final: 0.7682 (pp)
REVERT: B  232 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.7529 (mtt-85)
REVERT: B  270 LYS cc_start: 0.8788 (tttt) cc_final: 0.8560 (tttt)
REVERT: C   46 ARG cc_start: 0.6715 (ttm170) cc_final: 0.5840 (ttt90)
REVERT: C   51 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6952 (mp)
REVERT: C   87 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8587 (mm-40)
REVERT: C  194 LYS cc_start: 0.8208 (tppt) cc_final: 0.7799 (tptp)
REVERT: C  270 LYS cc_start: 0.8874 (tttt) cc_final: 0.8455 (tttp)
REVERT: D   46 ARG cc_start: 0.6436 (ttm170) cc_final: 0.5542 (ttp80)
REVERT: D   51 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6993 (mp)
REVERT: D   95 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7643 (mt)
REVERT: D  154 ASP cc_start: 0.7709 (t70) cc_final: 0.7377 (t0)
REVERT: D  206 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7974 (t70)
REVERT: D  232 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7652 (mtt-85)
REVERT: E   46 ARG cc_start: 0.6285 (ttm170) cc_final: 0.5447 (ttp80)
REVERT: E   51 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7044 (mp)
REVERT: E  154 ASP cc_start: 0.7821 (t70) cc_final: 0.7372 (t0)
REVERT: E  206 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7969 (t70)
REVERT: F   46 ARG cc_start: 0.6483 (ttm110) cc_final: 0.6226 (mtp-110)
REVERT: F   51 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6905 (mp)
REVERT: F   87 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8293 (mm-40)
REVERT: F  154 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7490 (t70)
REVERT: G   46 ARG cc_start: 0.6417 (ttm170) cc_final: 0.5667 (ttt-90)
REVERT: G   51 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.6999 (mp)
REVERT: G   95 ILE cc_start: 0.8088 (mp) cc_final: 0.7847 (mt)
REVERT: G  154 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7206 (t70)
REVERT: G  206 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7767 (t70)
REVERT: G  239 ASP cc_start: 0.9122 (m-30) cc_final: 0.8883 (m-30)
REVERT: G  270 LYS cc_start: 0.8771 (tttt) cc_final: 0.8293 (tttp)
  outliers start: 44
  outliers final: 27
  residues processed: 250
  average time/residue: 0.5892
  time to fit residues: 160.2921
Evaluate side-chains
  251 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 211
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  126 LYS
Chi-restraints excluded: chain A residue  174 SER
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   90 SER
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  232 ARG
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   57 ASP
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  109 SER
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  272 VAL
Chi-restraints excluded: chain C residue  273 GLN
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   57 ASP
Chi-restraints excluded: chain D residue   95 ILE
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  206 ASP
Chi-restraints excluded: chain D residue  232 ARG
Chi-restraints excluded: chain D residue  272 VAL
Chi-restraints excluded: chain D residue  273 GLN
Chi-restraints excluded: chain E residue   51 LEU
Chi-restraints excluded: chain E residue  109 SER
Chi-restraints excluded: chain E residue  206 ASP
Chi-restraints excluded: chain E residue  272 VAL
Chi-restraints excluded: chain E residue  273 GLN
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue  109 SER
Chi-restraints excluded: chain F residue  154 ASP
Chi-restraints excluded: chain F residue  272 VAL
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain G residue   57 ASP
Chi-restraints excluded: chain G residue  109 SER
Chi-restraints excluded: chain G residue  154 ASP
Chi-restraints excluded: chain G residue  206 ASP
Chi-restraints excluded: chain G residue  272 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 97 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 87 optimal weight:    0.9980
   chunk 130 optimal weight:   30.0000
   chunk 131 optimal weight:    0.9980
   chunk 22 optimal weight:    0.4980
   chunk 128 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 152 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B 197 GLN
C 197 GLN
F 197 GLN
G  41 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.135157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.099705 restraints weight = 15723.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 1.80
r_work: 0.3039 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2915 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13972  Z= 0.129
  Angle     :  0.591   8.148  19033  Z= 0.317
  Chirality :  0.044   0.184   2324
  Planarity :  0.005   0.066   2380
  Dihedral  :  4.730  36.734   1939
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.78 %
    Allowed  :  6.20 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 24.04 %
    Favored  : 73.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.61 (0.21), residues: 1806
  helix:  2.36 (0.17), residues: 959
  sheet: -0.52 (0.30), residues: 280
  loop : -0.30 (0.29), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  54 
 TYR   0.009   0.001   TYR E 173 
 PHE   0.011   0.001   PHE C  63 
 TRP   0.006   0.001   TRP C 241 
 HIS   0.002   0.001   HIS F 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (13972)
  covalent geometry    : angle       0.59091 (19033)
  hydrogen bonds       : bond        0.04705 (  929)
  hydrogen bonds       : angle       3.60954 ( 2745)

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

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

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 211
  time to evaluate  : 0.514 
Fit side-chains
REVERT: A   46 ARG cc_start: 0.6382 (ttm170) cc_final: 0.5710 (ttt90)
REVERT: A   87 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8268 (mm-40)
REVERT: A  145 ILE cc_start: 0.7991 (mt) cc_final: 0.7711 (pp)
REVERT: A  195 ASN cc_start: 0.8590 (t0) cc_final: 0.8147 (t0)
REVERT: B   46 ARG cc_start: 0.6059 (ttm170) cc_final: 0.5270 (ttt90)
REVERT: B  145 ILE cc_start: 0.7999 (mt) cc_final: 0.7717 (pp)
REVERT: B  232 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.7549 (mtt-85)
REVERT: B  270 LYS cc_start: 0.8786 (tttt) cc_final: 0.8559 (tttt)
REVERT: C   46 ARG cc_start: 0.6712 (ttm170) cc_final: 0.5836 (ttt90)
REVERT: C   51 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6927 (mp)
REVERT: C  194 LYS cc_start: 0.8205 (tppt) cc_final: 0.7804 (tptp)
REVERT: C  270 LYS cc_start: 0.8874 (tttt) cc_final: 0.8452 (tttp)
REVERT: D   46 ARG cc_start: 0.6433 (ttm170) cc_final: 0.5538 (ttp80)
REVERT: D   51 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6906 (mp)
REVERT: D   95 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7616 (mt)
REVERT: D  154 ASP cc_start: 0.7689 (t70) cc_final: 0.7357 (t0)
REVERT: D  206 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7961 (t70)
REVERT: D  232 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7648 (mtt-85)
REVERT: E   46 ARG cc_start: 0.6289 (ttm170) cc_final: 0.5451 (ttp80)
REVERT: E   51 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7047 (mp)
REVERT: E  154 ASP cc_start: 0.7722 (t70) cc_final: 0.7429 (t0)
REVERT: E  206 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7967 (t70)
REVERT: F   46 ARG cc_start: 0.6456 (ttm110) cc_final: 0.6193 (mtp-110)
REVERT: F   51 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6925 (mp)
REVERT: F   87 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8288 (mm-40)
REVERT: F  154 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7481 (t70)
REVERT: G   46 ARG cc_start: 0.6427 (ttm170) cc_final: 0.5675 (ttt-90)
REVERT: G   51 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6975 (mp)
REVERT: G   95 ILE cc_start: 0.8084 (mp) cc_final: 0.7843 (mt)
REVERT: G  154 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7229 (t70)
REVERT: G  206 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7767 (t70)
REVERT: G  270 LYS cc_start: 0.8772 (tttt) cc_final: 0.8293 (tttp)
  outliers start: 41
  outliers final: 27
  residues processed: 243
  average time/residue: 0.6006
  time to fit residues: 158.6799
Evaluate side-chains
  250 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 210
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  126 LYS
Chi-restraints excluded: chain A residue  174 SER
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   90 SER
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  232 ARG
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   57 ASP
Chi-restraints excluded: chain C residue  109 SER
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  272 VAL
Chi-restraints excluded: chain C residue  273 GLN
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   95 ILE
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  206 ASP
Chi-restraints excluded: chain D residue  232 ARG
Chi-restraints excluded: chain D residue  272 VAL
Chi-restraints excluded: chain D residue  273 GLN
Chi-restraints excluded: chain E residue   51 LEU
Chi-restraints excluded: chain E residue   57 ASP
Chi-restraints excluded: chain E residue  109 SER
Chi-restraints excluded: chain E residue  206 ASP
Chi-restraints excluded: chain E residue  272 VAL
Chi-restraints excluded: chain E residue  273 GLN
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue   57 ASP
Chi-restraints excluded: chain F residue  109 SER
Chi-restraints excluded: chain F residue  154 ASP
Chi-restraints excluded: chain F residue  272 VAL
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain G residue  109 SER
Chi-restraints excluded: chain G residue  154 ASP
Chi-restraints excluded: chain G residue  206 ASP
Chi-restraints excluded: chain G residue  272 VAL
Chi-restraints excluded: chain G residue  273 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 137 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 180 optimal weight:    0.0970
   chunk 24 optimal weight:    6.9990
   chunk 158 optimal weight:    7.9990
   chunk 80 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9990
   chunk 50 optimal weight:    6.9990
   chunk 129 optimal weight:    0.3980
   chunk 181 optimal weight:    0.6980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B 197 GLN
C 197 GLN
F 197 GLN
G  41 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.134891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.100282 restraints weight = 15832.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 1.75
r_work: 0.3045 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13972  Z= 0.127
  Angle     :  0.586   8.115  19033  Z= 0.314
  Chirality :  0.044   0.192   2324
  Planarity :  0.005   0.065   2380
  Dihedral  :  4.721  35.973   1939
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.78 %
    Allowed  :  6.15 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 24.18 %
    Favored  : 73.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.63 (0.21), residues: 1806
  helix:  2.38 (0.17), residues: 959
  sheet: -0.49 (0.30), residues: 280
  loop : -0.31 (0.29), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  54 
 TYR   0.008   0.001   TYR E 173 
 PHE   0.011   0.001   PHE C  63 
 TRP   0.006   0.001   TRP C 241 
 HIS   0.002   0.001   HIS B 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (13972)
  covalent geometry    : angle       0.58608 (19033)
  hydrogen bonds       : bond        0.04670 (  929)
  hydrogen bonds       : angle       3.60979 ( 2745)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5900.12 seconds
wall clock time: 100 minutes 29.48 seconds (6029.48 seconds total)