Starting phenix.real_space_refine
on Thu Mar  5 01:58:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f3e_31432/03_2026/7f3e_31432.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f3e_31432/03_2026/7f3e_31432.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f3e_31432/03_2026/7f3e_31432.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f3e_31432/03_2026/7f3e_31432.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f3e_31432/03_2026/7f3e_31432.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f3e_31432/03_2026/7f3e_31432.map"
  }
  resolution = 3.62
  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=  -0.000 sd=   0.009
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      84      5.16       5
     C   11868      2.51       5
     N    3168      2.21       5
     O    3444      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 96 residue(s): 0.02s

  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: 18564
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "E"
      Number of atoms: 1547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 1547
          Classifications: {'peptide': 188}
          Link IDs: {'PTRANS': 5, 'TRANS': 182}
          Chain breaks: 1
  Restraints were copied for chains:
    F, C, D, A, B, H, G, J, I, L, K
  Time building chain proxies: 1.99, per 1000 atoms: 0.11
  Number of scatterers: 18564
  At special positions: 0
  Unit cell: (102.96, 157.52, 136.4, 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      84     16.00
     O    3444      8.00
     N    3168      7.00
     C   11868      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.72
  Conformation dependent library (CDL) restraints added in 736.8 milliseconds
  

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4296

  Finding SS restraints...
    Secondary structure from input PDB file:
      120 helices and 18 sheets defined
      70.2% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'E' and resid 7 through 11
      removed outlier: 3.969A  pdb=" N   VAL E  10 " --> pdb=" O   ASP E   7 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE E  11 " --> pdb=" O   THR E   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 7 through 11'
    Processing helix  chain 'E' and resid 13 through 20
    Processing helix  chain 'E' and resid 26 through 37
      removed outlier: 3.741A  pdb=" N   ASN E  37 " --> pdb=" O   HIS E  33 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 56
    Processing helix  chain 'E' and resid 61 through 68
      removed outlier: 3.873A  pdb=" N   PHE E  65 " --> pdb=" O   LEU E  61 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 83 through 114
      removed outlier: 3.838A  pdb=" N   TYR E  95 " --> pdb=" O   GLU E  91 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 116 through 133
    Processing helix  chain 'E' and resid 139 through 152
      removed outlier: 4.012A  pdb=" N   VAL E 143 " --> pdb=" O   SER E 139 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU E 152 " --> pdb=" O   LEU E 148 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 160 through 171
      removed outlier: 4.166A  pdb=" N   THR E 165 " --> pdb=" O   GLU E 161 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TRP E 166 " --> pdb=" O   GLY E 162 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 179 through 190
    Processing helix  chain 'F' and resid 7 through 11
      removed outlier: 3.969A  pdb=" N   VAL F  10 " --> pdb=" O   ASP F   7 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE F  11 " --> pdb=" O   THR F   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 7 through 11'
    Processing helix  chain 'F' and resid 13 through 20
    Processing helix  chain 'F' and resid 26 through 37
      removed outlier: 3.741A  pdb=" N   ASN F  37 " --> pdb=" O   HIS F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 46 through 56
    Processing helix  chain 'F' and resid 61 through 68
      removed outlier: 3.873A  pdb=" N   PHE F  65 " --> pdb=" O   LEU F  61 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 83 through 114
      removed outlier: 3.838A  pdb=" N   TYR F  95 " --> pdb=" O   GLU F  91 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 116 through 133
    Processing helix  chain 'F' and resid 139 through 152
      removed outlier: 4.012A  pdb=" N   VAL F 143 " --> pdb=" O   SER F 139 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU F 152 " --> pdb=" O   LEU F 148 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 160 through 171
      removed outlier: 4.165A  pdb=" N   THR F 165 " --> pdb=" O   GLU F 161 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TRP F 166 " --> pdb=" O   GLY F 162 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 179 through 190
    Processing helix  chain 'C' and resid 7 through 11
      removed outlier: 3.969A  pdb=" N   VAL C  10 " --> pdb=" O   ASP C   7 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   PHE C  11 " --> pdb=" O   THR C   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 7 through 11'
    Processing helix  chain 'C' and resid 13 through 20
    Processing helix  chain 'C' and resid 26 through 37
      removed outlier: 3.743A  pdb=" N   ASN C  37 " --> pdb=" O   HIS C  33 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 56
    Processing helix  chain 'C' and resid 61 through 68
      removed outlier: 3.873A  pdb=" N   PHE C  65 " --> pdb=" O   LEU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 83 through 114
      removed outlier: 3.838A  pdb=" N   TYR C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 116 through 133
    Processing helix  chain 'C' and resid 139 through 152
      removed outlier: 4.012A  pdb=" N   VAL C 143 " --> pdb=" O   SER C 139 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU C 152 " --> pdb=" O   LEU C 148 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 160 through 171
      removed outlier: 4.165A  pdb=" N   THR C 165 " --> pdb=" O   GLU C 161 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TRP C 166 " --> pdb=" O   GLY C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 190
    Processing helix  chain 'D' and resid 7 through 11
      removed outlier: 3.969A  pdb=" N   VAL D  10 " --> pdb=" O   ASP D   7 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE D  11 " --> pdb=" O   THR D   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 7 through 11'
    Processing helix  chain 'D' and resid 13 through 20
    Processing helix  chain 'D' and resid 26 through 37
      removed outlier: 3.740A  pdb=" N   ASN D  37 " --> pdb=" O   HIS D  33 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 46 through 56
    Processing helix  chain 'D' and resid 61 through 68
      removed outlier: 3.874A  pdb=" N   PHE D  65 " --> pdb=" O   LEU D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 83 through 114
      removed outlier: 3.837A  pdb=" N   TYR D  95 " --> pdb=" O   GLU D  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 116 through 133
    Processing helix  chain 'D' and resid 139 through 152
      removed outlier: 4.013A  pdb=" N   VAL D 143 " --> pdb=" O   SER D 139 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU D 152 " --> pdb=" O   LEU D 148 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 160 through 171
      removed outlier: 4.164A  pdb=" N   THR D 165 " --> pdb=" O   GLU D 161 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   TRP D 166 " --> pdb=" O   GLY D 162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 179 through 190
    Processing helix  chain 'A' and resid 7 through 11
      removed outlier: 3.970A  pdb=" N   VAL A  10 " --> pdb=" O   ASP A   7 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   PHE A  11 " --> pdb=" O   THR A   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 7 through 11'
    Processing helix  chain 'A' and resid 13 through 20
    Processing helix  chain 'A' and resid 26 through 37
      removed outlier: 3.742A  pdb=" N   ASN A  37 " --> pdb=" O   HIS A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 56
    Processing helix  chain 'A' and resid 61 through 68
      removed outlier: 3.873A  pdb=" N   PHE A  65 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 114
      removed outlier: 3.839A  pdb=" N   TYR A  95 " --> pdb=" O   GLU A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 133
    Processing helix  chain 'A' and resid 139 through 152
      removed outlier: 4.012A  pdb=" N   VAL A 143 " --> pdb=" O   SER A 139 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU A 152 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 171
      removed outlier: 4.166A  pdb=" N   THR A 165 " --> pdb=" O   GLU A 161 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   TRP A 166 " --> pdb=" O   GLY A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 190
    Processing helix  chain 'B' and resid 7 through 11
      removed outlier: 3.969A  pdb=" N   VAL B  10 " --> pdb=" O   ASP B   7 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   PHE B  11 " --> pdb=" O   THR B   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 7 through 11'
    Processing helix  chain 'B' and resid 13 through 20
    Processing helix  chain 'B' and resid 26 through 37
      removed outlier: 3.742A  pdb=" N   ASN B  37 " --> pdb=" O   HIS B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 56
    Processing helix  chain 'B' and resid 61 through 68
      removed outlier: 3.872A  pdb=" N   PHE B  65 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 114
      removed outlier: 3.838A  pdb=" N   TYR B  95 " --> pdb=" O   GLU B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 133
    Processing helix  chain 'B' and resid 139 through 152
      removed outlier: 4.014A  pdb=" N   VAL B 143 " --> pdb=" O   SER B 139 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU B 152 " --> pdb=" O   LEU B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 171
      removed outlier: 4.164A  pdb=" N   THR B 165 " --> pdb=" O   GLU B 161 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TRP B 166 " --> pdb=" O   GLY B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 190
    Processing helix  chain 'H' and resid 7 through 11
      removed outlier: 3.969A  pdb=" N   VAL H  10 " --> pdb=" O   ASP H   7 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE H  11 " --> pdb=" O   THR H   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 7 through 11'
    Processing helix  chain 'H' and resid 13 through 20
    Processing helix  chain 'H' and resid 26 through 37
      removed outlier: 3.742A  pdb=" N   ASN H  37 " --> pdb=" O   HIS H  33 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 46 through 56
    Processing helix  chain 'H' and resid 61 through 68
      removed outlier: 3.874A  pdb=" N   PHE H  65 " --> pdb=" O   LEU H  61 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 83 through 114
      removed outlier: 3.837A  pdb=" N   TYR H  95 " --> pdb=" O   GLU H  91 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 116 through 133
    Processing helix  chain 'H' and resid 139 through 152
      removed outlier: 4.012A  pdb=" N   VAL H 143 " --> pdb=" O   SER H 139 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU H 152 " --> pdb=" O   LEU H 148 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 160 through 171
      removed outlier: 4.166A  pdb=" N   THR H 165 " --> pdb=" O   GLU H 161 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   TRP H 166 " --> pdb=" O   GLY H 162 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 179 through 190
    Processing helix  chain 'G' and resid 7 through 11
      removed outlier: 3.969A  pdb=" N   VAL G  10 " --> pdb=" O   ASP G   7 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE G  11 " --> pdb=" O   THR G   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 7 through 11'
    Processing helix  chain 'G' and resid 13 through 20
    Processing helix  chain 'G' and resid 26 through 37
      removed outlier: 3.742A  pdb=" N   ASN G  37 " --> pdb=" O   HIS G  33 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 56
    Processing helix  chain 'G' and resid 61 through 68
      removed outlier: 3.874A  pdb=" N   PHE G  65 " --> pdb=" O   LEU G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 83 through 114
      removed outlier: 3.838A  pdb=" N   TYR G  95 " --> pdb=" O   GLU G  91 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 116 through 133
    Processing helix  chain 'G' and resid 139 through 152
      removed outlier: 4.012A  pdb=" N   VAL G 143 " --> pdb=" O   SER G 139 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU G 152 " --> pdb=" O   LEU G 148 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 160 through 171
      removed outlier: 4.164A  pdb=" N   THR G 165 " --> pdb=" O   GLU G 161 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TRP G 166 " --> pdb=" O   GLY G 162 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 179 through 190
    Processing helix  chain 'J' and resid 7 through 11
      removed outlier: 3.970A  pdb=" N   VAL J  10 " --> pdb=" O   ASP J   7 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE J  11 " --> pdb=" O   THR J   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 7 through 11'
    Processing helix  chain 'J' and resid 13 through 20
    Processing helix  chain 'J' and resid 26 through 37
      removed outlier: 3.742A  pdb=" N   ASN J  37 " --> pdb=" O   HIS J  33 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 46 through 56
    Processing helix  chain 'J' and resid 61 through 68
      removed outlier: 3.873A  pdb=" N   PHE J  65 " --> pdb=" O   LEU J  61 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 83 through 114
      removed outlier: 3.838A  pdb=" N   TYR J  95 " --> pdb=" O   GLU J  91 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 116 through 133
    Processing helix  chain 'J' and resid 139 through 152
      removed outlier: 4.012A  pdb=" N   VAL J 143 " --> pdb=" O   SER J 139 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU J 152 " --> pdb=" O   LEU J 148 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 160 through 171
      removed outlier: 4.166A  pdb=" N   THR J 165 " --> pdb=" O   GLU J 161 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TRP J 166 " --> pdb=" O   GLY J 162 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 179 through 190
    Processing helix  chain 'I' and resid 7 through 11
      removed outlier: 3.969A  pdb=" N   VAL I  10 " --> pdb=" O   ASP I   7 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE I  11 " --> pdb=" O   THR I   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 7 through 11'
    Processing helix  chain 'I' and resid 13 through 20
    Processing helix  chain 'I' and resid 26 through 37
      removed outlier: 3.742A  pdb=" N   ASN I  37 " --> pdb=" O   HIS I  33 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 46 through 56
    Processing helix  chain 'I' and resid 61 through 68
      removed outlier: 3.872A  pdb=" N   PHE I  65 " --> pdb=" O   LEU I  61 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 83 through 114
      removed outlier: 3.838A  pdb=" N   TYR I  95 " --> pdb=" O   GLU I  91 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 116 through 133
    Processing helix  chain 'I' and resid 139 through 152
      removed outlier: 4.013A  pdb=" N   VAL I 143 " --> pdb=" O   SER I 139 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU I 152 " --> pdb=" O   LEU I 148 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 160 through 171
      removed outlier: 4.165A  pdb=" N   THR I 165 " --> pdb=" O   GLU I 161 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   TRP I 166 " --> pdb=" O   GLY I 162 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 179 through 190
    Processing helix  chain 'L' and resid 7 through 11
      removed outlier: 3.970A  pdb=" N   VAL L  10 " --> pdb=" O   ASP L   7 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   PHE L  11 " --> pdb=" O   THR L   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 7 through 11'
    Processing helix  chain 'L' and resid 13 through 20
    Processing helix  chain 'L' and resid 26 through 37
      removed outlier: 3.742A  pdb=" N   ASN L  37 " --> pdb=" O   HIS L  33 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 46 through 56
    Processing helix  chain 'L' and resid 61 through 68
      removed outlier: 3.875A  pdb=" N   PHE L  65 " --> pdb=" O   LEU L  61 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 83 through 114
      removed outlier: 3.840A  pdb=" N   TYR L  95 " --> pdb=" O   GLU L  91 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 116 through 133
    Processing helix  chain 'L' and resid 139 through 152
      removed outlier: 4.013A  pdb=" N   VAL L 143 " --> pdb=" O   SER L 139 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU L 152 " --> pdb=" O   LEU L 148 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 160 through 171
      removed outlier: 4.166A  pdb=" N   THR L 165 " --> pdb=" O   GLU L 161 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TRP L 166 " --> pdb=" O   GLY L 162 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 179 through 190
    Processing helix  chain 'K' and resid 7 through 11
      removed outlier: 3.969A  pdb=" N   VAL K  10 " --> pdb=" O   ASP K   7 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE K  11 " --> pdb=" O   THR K   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 7 through 11'
    Processing helix  chain 'K' and resid 13 through 20
    Processing helix  chain 'K' and resid 26 through 37
      removed outlier: 3.742A  pdb=" N   ASN K  37 " --> pdb=" O   HIS K  33 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 46 through 56
    Processing helix  chain 'K' and resid 61 through 68
      removed outlier: 3.874A  pdb=" N   PHE K  65 " --> pdb=" O   LEU K  61 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 83 through 114
      removed outlier: 3.839A  pdb=" N   TYR K  95 " --> pdb=" O   GLU K  91 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 116 through 133
    Processing helix  chain 'K' and resid 139 through 152
      removed outlier: 4.012A  pdb=" N   VAL K 143 " --> pdb=" O   SER K 139 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU K 152 " --> pdb=" O   LEU K 148 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 160 through 171
      removed outlier: 4.165A  pdb=" N   THR K 165 " --> pdb=" O   GLU K 161 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TRP K 166 " --> pdb=" O   GLY K 162 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 179 through 190
    Processing sheet with id=AA1, first strand: chain 'E' and resid 69 through 72
      removed outlier: 3.861A  pdb=" N   LYS E  70 " --> pdb=" O   PHE E  42 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   PHE E   4 " --> pdb=" O   TYR E  43 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 80 through 82
    Processing sheet with id=AA3, first strand: chain 'F' and resid 69 through 72
      removed outlier: 3.861A  pdb=" N   LYS F  70 " --> pdb=" O   PHE F  42 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   PHE F   4 " --> pdb=" O   TYR F  43 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 69 through 72
      removed outlier: 3.861A  pdb=" N   LYS C  70 " --> pdb=" O   PHE C  42 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   PHE C   4 " --> pdb=" O   TYR C  43 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 80 through 82
    Processing sheet with id=AA6, first strand: chain 'D' and resid 69 through 72
      removed outlier: 3.860A  pdb=" N   LYS D  70 " --> pdb=" O   PHE D  42 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   PHE D   4 " --> pdb=" O   TYR D  43 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 69 through 72
      removed outlier: 3.861A  pdb=" N   LYS A  70 " --> pdb=" O   PHE A  42 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   PHE A   4 " --> pdb=" O   TYR A  43 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 80 through 82
    Processing sheet with id=AA9, first strand: chain 'B' and resid 69 through 72
      removed outlier: 3.861A  pdb=" N   LYS B  70 " --> pdb=" O   PHE B  42 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   PHE B   4 " --> pdb=" O   TYR B  43 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 69 through 72
      removed outlier: 3.860A  pdb=" N   LYS H  70 " --> pdb=" O   PHE H  42 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   PHE H   4 " --> pdb=" O   TYR H  43 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 80 through 82
    Processing sheet with id=AB3, first strand: chain 'G' and resid 69 through 72
      removed outlier: 3.862A  pdb=" N   LYS G  70 " --> pdb=" O   PHE G  42 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   PHE G   4 " --> pdb=" O   TYR G  43 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'J' and resid 69 through 72
      removed outlier: 3.860A  pdb=" N   LYS J  70 " --> pdb=" O   PHE J  42 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   PHE J   4 " --> pdb=" O   TYR J  43 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'J' and resid 80 through 82
    Processing sheet with id=AB6, first strand: chain 'I' and resid 69 through 72
      removed outlier: 3.860A  pdb=" N   LYS I  70 " --> pdb=" O   PHE I  42 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   PHE I   4 " --> pdb=" O   TYR I  43 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 69 through 72
      removed outlier: 3.861A  pdb=" N   LYS L  70 " --> pdb=" O   PHE L  42 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   PHE L   4 " --> pdb=" O   TYR L  43 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 80 through 82
    Processing sheet with id=AB9, first strand: chain 'K' and resid 69 through 72
      removed outlier: 3.861A  pdb=" N   LYS K  70 " --> pdb=" O   PHE K  42 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   PHE K   4 " --> pdb=" O   TYR K  43 " (cutoff:3.500A)

    1056 hydrogen bonds defined for protein.
    3168 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.42

  Time building geometry restraints manager: 2.30 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 6156
        1.34 -     1.46: 3204
        1.46 -     1.57: 9372
        1.57 -     1.69: 0
        1.69 -     1.81: 156
  Bond restraints: 18888
  Sorted by residual:
  bond pdb=" CB  VAL L 143 "
       pdb=" CG2 VAL L 143 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.06e+00
  bond pdb=" CG1 ILE I  90 "
       pdb=" CD1 ILE I  90 "
    ideal  model  delta    sigma   weight residual
    1.513  1.473  0.040 3.90e-02 6.57e+02 1.03e+00
  bond pdb=" CB  VAL C 143 "
       pdb=" CG2 VAL C 143 "
    ideal  model  delta    sigma   weight residual
    1.521  1.488  0.033 3.30e-02 9.18e+02 1.01e+00
  bond pdb=" CG1 ILE K  90 "
       pdb=" CD1 ILE K  90 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 1.01e+00
  bond pdb=" CB  VAL B 143 "
       pdb=" CG2 VAL B 143 "
    ideal  model  delta    sigma   weight residual
    1.521  1.488  0.033 3.30e-02 9.18e+02 1.01e+00
  ... (remaining 18883 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 22717
        1.04 -     2.07: 2273
        2.07 -     3.11: 278
        3.11 -     4.14: 105
        4.14 -     5.18: 55
  Bond angle restraints: 25428
  Sorted by residual:
  angle pdb=" N   THR K  12 "
        pdb=" CA  THR K  12 "
        pdb=" C   THR K  12 "
      ideal   model   delta    sigma   weight residual
     114.56  111.72    2.84 1.27e+00 6.20e-01 4.98e+00
  angle pdb=" N   THR I  12 "
        pdb=" CA  THR I  12 "
        pdb=" C   THR I  12 "
      ideal   model   delta    sigma   weight residual
     114.56  111.76    2.80 1.27e+00 6.20e-01 4.87e+00
  angle pdb=" N   THR L  12 "
        pdb=" CA  THR L  12 "
        pdb=" C   THR L  12 "
      ideal   model   delta    sigma   weight residual
     114.56  111.76    2.80 1.27e+00 6.20e-01 4.85e+00
  angle pdb=" N   GLU I  60 "
        pdb=" CA  GLU I  60 "
        pdb=" CB  GLU I  60 "
      ideal   model   delta    sigma   weight residual
     113.65  110.42    3.23 1.47e+00 4.63e-01 4.83e+00
  angle pdb=" N   THR E  12 "
        pdb=" CA  THR E  12 "
        pdb=" C   THR E  12 "
      ideal   model   delta    sigma   weight residual
     114.56  111.77    2.79 1.27e+00 6.20e-01 4.82e+00
  ... (remaining 25423 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.72: 9739
       14.72 -    29.44: 1301
       29.44 -    44.16: 312
       44.16 -    58.88: 108
       58.88 -    73.60: 48
  Dihedral angle restraints: 11508
    sinusoidal: 4896
      harmonic: 6612
  Sorted by residual:
  dihedral pdb=" CA  PHE B  11 "
           pdb=" C   PHE B  11 "
           pdb=" N   THR B  12 "
           pdb=" CA  THR B  12 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.64   21.36     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  PHE J  11 "
           pdb=" C   PHE J  11 "
           pdb=" N   THR J  12 "
           pdb=" CA  THR J  12 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.66   21.34     0      5.00e+00 4.00e-02 1.82e+01
  dihedral pdb=" CA  PHE E  11 "
           pdb=" C   PHE E  11 "
           pdb=" N   THR E  12 "
           pdb=" CA  THR E  12 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.67   21.33     0      5.00e+00 4.00e-02 1.82e+01
  ... (remaining 11505 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1706
       0.033 -    0.066: 747
       0.066 -    0.099: 242
       0.099 -    0.131: 101
       0.131 -    0.164: 36
  Chirality restraints: 2832
  Sorted by residual:
  chirality pdb=" CB  ILE F  16 "
            pdb=" CA  ILE F  16 "
            pdb=" CG1 ILE F  16 "
            pdb=" CG2 ILE F  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.81   -0.16 2.00e-01 2.50e+01 6.75e-01
  chirality pdb=" CB  ILE C  16 "
            pdb=" CA  ILE C  16 "
            pdb=" CG1 ILE C  16 "
            pdb=" CG2 ILE C  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.81   -0.16 2.00e-01 2.50e+01 6.65e-01
  chirality pdb=" CB  ILE G  16 "
            pdb=" CA  ILE G  16 "
            pdb=" CG1 ILE G  16 "
            pdb=" CG2 ILE G  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.81   -0.16 2.00e-01 2.50e+01 6.63e-01
  ... (remaining 2829 not shown)

  Planarity restraints: 3252
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER G  73 "   -0.039 5.00e-02 4.00e+02   5.89e-02 5.56e+00
        pdb=" N   PRO G  74 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO G  74 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO G  74 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER F  73 "    0.038 5.00e-02 4.00e+02   5.88e-02 5.54e+00
        pdb=" N   PRO F  74 "   -0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO F  74 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO F  74 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D  73 "    0.038 5.00e-02 4.00e+02   5.88e-02 5.53e+00
        pdb=" N   PRO D  74 "   -0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO D  74 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO D  74 "    0.033 5.00e-02 4.00e+02
  ... (remaining 3249 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 3704
        2.77 -     3.30: 18450
        3.30 -     3.84: 29189
        3.84 -     4.37: 34003
        4.37 -     4.90: 58577
  Nonbonded interactions: 143923
  Sorted by model distance:
  nonbonded pdb=" O   GLU K 105 "
            pdb=" OG1 THR K 108 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   GLU B 105 "
            pdb=" OG1 THR B 108 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   GLU D 105 "
            pdb=" OG1 THR D 108 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   GLU J 105 "
            pdb=" OG1 THR J 108 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   GLU A 105 "
            pdb=" OG1 THR A 108 "
     model   vdw
     2.243 3.040
  ... (remaining 143918 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'A'
  selection = chain 'B'
  selection = chain 'H'
  selection = chain 'G'
  selection = chain 'J'
  selection = chain 'I'
  selection = chain 'L'
  selection = chain 'K'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     15.300
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   19.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6489
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  18888  Z= 0.217
  Angle     :  0.709   5.179  25428  Z= 0.426
  Chirality :  0.045   0.164   2832
  Planarity :  0.005   0.059   3252
  Dihedral  : 15.180  73.599   7212
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.05 %
    Favored  : 99.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.41 (0.17), residues: 2208
  helix:  0.86 (0.14), residues: 1428
  sheet:  None (None), residues: 0
  loop : -2.50 (0.18), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  18 
 TYR   0.012   0.002   TYR B 128 
 PHE   0.014   0.002   PHE A  31 
 TRP   0.014   0.002   TRP D 166 
 HIS   0.002   0.001   HIS J  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 (18888)
  covalent geometry    : angle       0.70889 (25428)
  hydrogen bonds       : bond        0.18845 ( 1056)
  hydrogen bonds       : angle       6.16552 ( 3168)

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  453 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 453
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   13 ASN cc_start: 0.5555 (t0) cc_final: 0.5289 (m-40)
REVERT: C   51 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6170 (mm-30)
REVERT: D   55 ILE cc_start: 0.7123 (mt) cc_final: 0.6549 (mt)
REVERT: D  160 ASP cc_start: 0.7527 (t70) cc_final: 0.6260 (m-30)
REVERT: J   13 ASN cc_start: 0.5631 (t0) cc_final: 0.5373 (m-40)
REVERT: J   51 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6185 (mm-30)
REVERT: J   98 ASN cc_start: 0.7757 (m-40) cc_final: 0.7532 (m-40)
REVERT: I   55 ILE cc_start: 0.7212 (mt) cc_final: 0.6678 (mt)
REVERT: I  160 ASP cc_start: 0.7614 (t70) cc_final: 0.6343 (m-30)
REVERT: L  160 ASP cc_start: 0.5788 (t70) cc_final: 0.5514 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 453
  average time/residue: 0.1379
  time to fit residues: 93.3819
Evaluate side-chains
  255 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 255
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 194 optimal weight:    0.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    0.5980
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    4.9990
   chunk 200 optimal weight:    2.9990
   chunk 212 optimal weight:    3.9990
   chunk 77 optimal weight:    7.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
C 190 HIS
** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 179 ASN
J 190 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4584 r_free = 0.4584 target = 0.232854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.215603 restraints weight = 22217.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.197707 restraints weight = 32845.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.196256 restraints weight = 33502.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.196218 restraints weight = 31899.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.197025 restraints weight = 28751.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.4168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  18888  Z= 0.184
  Angle     :  0.651   6.291  25428  Z= 0.354
  Chirality :  0.046   0.151   2832
  Planarity :  0.005   0.052   3252
  Dihedral  :  4.775  22.996   2520
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 11.73 %
    Favored  : 86.73 %
  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: -0.48 (0.17), residues: 2208
  helix:  0.79 (0.13), residues: 1500
  sheet: -1.91 (0.46), residues: 120
  loop : -2.86 (0.20), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 133 
 TYR   0.025   0.002   TYR K  87 
 PHE   0.022   0.002   PHE H  31 
 TRP   0.015   0.002   TRP L 166 
 HIS   0.009   0.001   HIS G  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 (18888)
  covalent geometry    : angle       0.65110 (25428)
  hydrogen bonds       : bond        0.05840 ( 1056)
  hydrogen bonds       : angle       4.38720 ( 3168)

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 280
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    7 ASP cc_start: 0.6659 (t70) cc_final: 0.6170 (t0)
REVERT: C   67 MET cc_start: 0.5274 (mmm) cc_final: 0.4852 (mpp)
REVERT: D    7 ASP cc_start: 0.7297 (t70) cc_final: 0.7005 (t0)
REVERT: D   51 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7687 (mt-10)
REVERT: A   56 MET cc_start: 0.6333 (ttt) cc_final: 0.6118 (ttm)
REVERT: B   56 MET cc_start: 0.5088 (ppp) cc_final: 0.4881 (ppp)
REVERT: B  153 ASP cc_start: 0.7365 (m-30) cc_final: 0.7094 (m-30)
REVERT: J   13 ASN cc_start: 0.6027 (t0) cc_final: 0.5760 (m-40)
REVERT: J   98 ASN cc_start: 0.7812 (m-40) cc_final: 0.7467 (m-40)
REVERT: I    7 ASP cc_start: 0.7262 (t70) cc_final: 0.6961 (t0)
REVERT: I   28 MET cc_start: 0.6823 (tpt) cc_final: 0.6465 (tpt)
REVERT: I   55 ILE cc_start: 0.7242 (mt) cc_final: 0.6885 (mt)
REVERT: L   56 MET cc_start: 0.6117 (ttt) cc_final: 0.5862 (ttm)
REVERT: L   62 TRP cc_start: 0.4802 (m100) cc_final: 0.4566 (m100)
REVERT: L  160 ASP cc_start: 0.6137 (t70) cc_final: 0.5480 (m-30)
REVERT: K    1 MET cc_start: 0.1463 (tpt) cc_final: 0.0942 (tpt)
REVERT: K   56 MET cc_start: 0.5197 (ppp) cc_final: 0.4938 (ppp)
  outliers start: 31
  outliers final: 23
  residues processed: 298
  average time/residue: 0.1331
  time to fit residues: 60.5054
Evaluate side-chains
  248 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 224
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    8 THR
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain C residue    8 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain H residue    8 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain G residue    8 THR
Chi-restraints excluded: chain G residue  106 GLU
Chi-restraints excluded: chain J residue    8 THR
Chi-restraints excluded: chain J residue   50 THR
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   56 MET
Chi-restraints excluded: chain I residue  130 GLU
Chi-restraints excluded: chain L residue   97 ILE
Chi-restraints excluded: chain L residue  132 LEU
Chi-restraints excluded: chain L residue  140 LYS
Chi-restraints excluded: chain K residue   46 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 39 optimal weight:    7.9990
   chunk 212 optimal weight:    5.9990
   chunk 135 optimal weight:    2.9990
   chunk 155 optimal weight:    2.9990
   chunk 186 optimal weight:    8.9990
   chunk 149 optimal weight:    0.2980
   chunk 2 optimal weight:    5.9990
   chunk 125 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0070
   chunk 124 optimal weight:    0.6980
   chunk 115 optimal weight:    0.8980
   overall best weight:    0.7800

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

Flipped N/Q/H residues before XYZ refinement:
C 179 ASN
** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 179 ASN
** I 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.240524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.228308 restraints weight = 22357.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.223879 restraints weight = 30470.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.221364 restraints weight = 48056.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.220983 restraints weight = 44793.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.220040 restraints weight = 34961.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.4460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6573
moved from start:          0.3263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  18888  Z= 0.127
  Angle     :  0.549   5.686  25428  Z= 0.300
  Chirality :  0.043   0.193   2832
  Planarity :  0.004   0.043   3252
  Dihedral  :  4.325  21.164   2520
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.32 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.18 (0.18), residues: 2208
  helix:  1.06 (0.14), residues: 1488
  sheet: -1.78 (0.44), residues: 120
  loop : -2.80 (0.20), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H 129 
 TYR   0.014   0.001   TYR K  87 
 PHE   0.021   0.001   PHE J  11 
 TRP   0.012   0.002   TRP B 166 
 HIS   0.009   0.001   HIS F  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (18888)
  covalent geometry    : angle       0.54854 (25428)
  hydrogen bonds       : bond        0.04483 ( 1056)
  hydrogen bonds       : angle       4.06213 ( 3168)

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 271
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   11 PHE cc_start: 0.4624 (OUTLIER) cc_final: 0.4231 (p90)
REVERT: D    7 ASP cc_start: 0.6774 (t70) cc_final: 0.6538 (t0)
REVERT: D   51 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7640 (mt-10)
REVERT: A   80 THR cc_start: 0.7399 (p) cc_final: 0.6965 (t)
REVERT: B   52 MET cc_start: 0.7660 (tmm) cc_final: 0.7047 (ttp)
REVERT: G  134 GLN cc_start: 0.7522 (tp-100) cc_final: 0.7180 (tt0)
REVERT: J   98 ASN cc_start: 0.7794 (m-40) cc_final: 0.7489 (m-40)
REVERT: I   64 GLU cc_start: 0.5463 (mm-30) cc_final: 0.5057 (mm-30)
REVERT: L  160 ASP cc_start: 0.5898 (t70) cc_final: 0.5681 (m-30)
  outliers start: 41
  outliers final: 26
  residues processed: 298
  average time/residue: 0.1289
  time to fit residues: 58.5375
Evaluate side-chains
  257 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 229
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   11 PHE
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   56 MET
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   56 MET
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain F residue  184 LEU
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  184 LEU
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   56 MET
Chi-restraints excluded: chain H residue  183 ILE
Chi-restraints excluded: chain G residue    8 THR
Chi-restraints excluded: chain G residue  106 GLU
Chi-restraints excluded: chain G residue  184 LEU
Chi-restraints excluded: chain J residue   67 MET
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   56 MET
Chi-restraints excluded: chain I residue  106 GLU
Chi-restraints excluded: chain I residue  184 LEU
Chi-restraints excluded: chain L residue  132 LEU
Chi-restraints excluded: chain K residue   46 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 181 optimal weight:    0.9980
   chunk 162 optimal weight:    6.9990
   chunk 40 optimal weight:    0.8980
   chunk 161 optimal weight:    5.9990
   chunk 71 optimal weight:    8.9990
   chunk 0 optimal weight:    5.9990
   chunk 204 optimal weight:    5.9990
   chunk 145 optimal weight:    0.6980
   chunk 114 optimal weight:    0.7980
   chunk 11 optimal weight:    5.9990
   chunk 16 optimal weight:    0.4980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C 179 ASN
C 182 ASN
** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 179 ASN
J 179 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.241392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.228458 restraints weight = 22222.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 69)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.210412 restraints weight = 32757.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.208542 restraints weight = 27182.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.208281 restraints weight = 27454.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.208809 restraints weight = 25112.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.4275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.3630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  18888  Z= 0.121
  Angle     :  0.530   7.047  25428  Z= 0.289
  Chirality :  0.042   0.128   2832
  Planarity :  0.004   0.040   3252
  Dihedral  :  4.219  20.878   2520
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 18.01 %
    Favored  : 79.39 %
  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: -0.06 (0.18), residues: 2208
  helix:  1.12 (0.14), residues: 1488
  sheet: -1.80 (0.41), residues: 120
  loop : -2.65 (0.20), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 129 
 TYR   0.023   0.001   TYR K  87 
 PHE   0.017   0.001   PHE H  11 
 TRP   0.011   0.001   TRP L  62 
 HIS   0.008   0.001   HIS F  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (18888)
  covalent geometry    : angle       0.52992 (25428)
  hydrogen bonds       : bond        0.04195 ( 1056)
  hydrogen bonds       : angle       3.97952 ( 3168)

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 246
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   11 PHE cc_start: 0.4538 (OUTLIER) cc_final: 0.4145 (p90)
REVERT: C   32 ILE cc_start: 0.5978 (OUTLIER) cc_final: 0.5756 (mm)
REVERT: C   67 MET cc_start: 0.5467 (mtt) cc_final: 0.5148 (mpp)
REVERT: D    7 ASP cc_start: 0.6758 (t70) cc_final: 0.6537 (t0)
REVERT: D   51 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7108 (mp0)
REVERT: D  178 LYS cc_start: 0.7360 (tppt) cc_final: 0.7089 (mtmm)
REVERT: A   80 THR cc_start: 0.7225 (p) cc_final: 0.6712 (t)
REVERT: B  126 GLU cc_start: 0.4872 (mm-30) cc_final: 0.3866 (pt0)
REVERT: B  176 ASP cc_start: 0.5897 (p0) cc_final: 0.5616 (p0)
REVERT: J   98 ASN cc_start: 0.7725 (m-40) cc_final: 0.7395 (m-40)
REVERT: I    1 MET cc_start: 0.1503 (tpt) cc_final: 0.1288 (tpt)
REVERT: I   64 GLU cc_start: 0.5888 (mm-30) cc_final: 0.5476 (mm-30)
REVERT: L  160 ASP cc_start: 0.6234 (t70) cc_final: 0.5740 (m-30)
REVERT: L  169 LYS cc_start: 0.7933 (tptp) cc_final: 0.7562 (tttp)
  outliers start: 52
  outliers final: 36
  residues processed: 281
  average time/residue: 0.1224
  time to fit residues: 53.8074
Evaluate side-chains
  269 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 230
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    8 THR
Chi-restraints excluded: chain E residue   11 PHE
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   56 MET
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   56 MET
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain F residue  183 ILE
Chi-restraints excluded: chain F residue  184 LEU
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  151 GLU
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  184 LEU
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   73 SER
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue  183 ILE
Chi-restraints excluded: chain G residue    8 THR
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain G residue  106 GLU
Chi-restraints excluded: chain G residue  183 ILE
Chi-restraints excluded: chain G residue  184 LEU
Chi-restraints excluded: chain J residue   67 MET
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   32 ILE
Chi-restraints excluded: chain I residue   56 MET
Chi-restraints excluded: chain I residue  106 GLU
Chi-restraints excluded: chain I residue  184 LEU
Chi-restraints excluded: chain L residue  132 LEU
Chi-restraints excluded: chain K residue   46 THR
Chi-restraints excluded: chain K residue   73 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 204 optimal weight:    1.9990
   chunk 92 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0770
   chunk 5 optimal weight:    2.9990
   chunk 89 optimal weight:    0.0670
   chunk 202 optimal weight:    0.9990
   chunk 52 optimal weight:    0.1980
   chunk 146 optimal weight:    3.9990
   chunk 114 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    0.4680

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

Flipped N/Q/H residues before XYZ refinement:
C  13 ASN
C 179 ASN
C 182 ASN
J 179 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4689 r_free = 0.4689 target = 0.244936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.232096 restraints weight = 22044.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 78)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.212878 restraints weight = 33008.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.212138 restraints weight = 35955.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.211901 restraints weight = 40156.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.213034 restraints weight = 33426.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.4316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6812
moved from start:          0.4005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  18888  Z= 0.106
  Angle     :  0.495   6.563  25428  Z= 0.270
  Chirality :  0.041   0.128   2832
  Planarity :  0.004   0.052   3252
  Dihedral  :  3.971  20.253   2520
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 18.46 %
    Favored  : 78.14 %
  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:  0.10 (0.18), residues: 2208
  helix:  1.20 (0.14), residues: 1488
  sheet: -1.80 (0.37), residues: 120
  loop : -2.46 (0.20), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H 129 
 TYR   0.025   0.001   TYR K  87 
 PHE   0.014   0.001   PHE H  11 
 TRP   0.012   0.001   TRP L  62 
 HIS   0.008   0.001   HIS F  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (18888)
  covalent geometry    : angle       0.49524 (25428)
  hydrogen bonds       : bond        0.03583 ( 1056)
  hydrogen bonds       : angle       3.86133 ( 3168)

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 257
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   11 PHE cc_start: 0.4386 (OUTLIER) cc_final: 0.4048 (p90)
REVERT: E   67 MET cc_start: 0.7135 (tmm) cc_final: 0.6888 (tmm)
REVERT: C   67 MET cc_start: 0.5465 (mtt) cc_final: 0.5040 (mpp)
REVERT: D   51 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.6970 (mp0)
REVERT: D  120 LEU cc_start: 0.6344 (mt) cc_final: 0.6118 (mt)
REVERT: A   70 LYS cc_start: 0.6922 (mppt) cc_final: 0.6586 (mmtm)
REVERT: A   80 THR cc_start: 0.7262 (p) cc_final: 0.6659 (t)
REVERT: B   11 PHE cc_start: 0.5620 (OUTLIER) cc_final: 0.5233 (p90)
REVERT: B   81 VAL cc_start: 0.6833 (OUTLIER) cc_final: 0.6627 (t)
REVERT: B  126 GLU cc_start: 0.4876 (mm-30) cc_final: 0.3936 (pt0)
REVERT: H   67 MET cc_start: 0.7153 (tmm) cc_final: 0.6900 (tmm)
REVERT: J   98 ASN cc_start: 0.7725 (m-40) cc_final: 0.7430 (m-40)
REVERT: I   64 GLU cc_start: 0.5940 (mm-30) cc_final: 0.5416 (mm-30)
REVERT: L   70 LYS cc_start: 0.7015 (mppt) cc_final: 0.6803 (mppt)
REVERT: L   80 THR cc_start: 0.7229 (p) cc_final: 0.6677 (t)
REVERT: L  160 ASP cc_start: 0.6167 (t70) cc_final: 0.5717 (m-30)
REVERT: K  180 PHE cc_start: 0.2879 (t80) cc_final: 0.2535 (t80)
  outliers start: 68
  outliers final: 36
  residues processed: 302
  average time/residue: 0.1280
  time to fit residues: 59.9813
Evaluate side-chains
  262 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 222
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   11 PHE
Chi-restraints excluded: chain E residue   12 THR
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   56 MET
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   56 MET
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain F residue  184 LEU
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  151 GLU
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue  184 LEU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   11 PHE
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   73 SER
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  103 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain H residue   12 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   56 MET
Chi-restraints excluded: chain H residue  183 ILE
Chi-restraints excluded: chain G residue    8 THR
Chi-restraints excluded: chain G residue   32 ILE
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain G residue  106 GLU
Chi-restraints excluded: chain G residue  183 ILE
Chi-restraints excluded: chain G residue  184 LEU
Chi-restraints excluded: chain J residue   67 MET
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue  184 LEU
Chi-restraints excluded: chain L residue  132 LEU
Chi-restraints excluded: chain K residue   46 THR
Chi-restraints excluded: chain K residue   73 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 103 optimal weight:    9.9990
   chunk 1 optimal weight:    0.8980
   chunk 49 optimal weight:    6.9990
   chunk 95 optimal weight:    8.9990
   chunk 194 optimal weight:    0.9980
   chunk 186 optimal weight:    7.9990
   chunk 200 optimal weight:    4.9990
   chunk 101 optimal weight:    0.0670
   chunk 147 optimal weight:    3.9990
   chunk 192 optimal weight:    4.9990
   chunk 178 optimal weight:    0.9990
   overall best weight:    1.3922

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

Flipped N/Q/H residues before XYZ refinement:
A 179 ASN
** I 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.238259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.224935 restraints weight = 21911.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.206678 restraints weight = 33328.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.205307 restraints weight = 26005.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.204672 restraints weight = 29191.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.205279 restraints weight = 27413.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.4230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6985
moved from start:          0.4117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  18888  Z= 0.143
  Angle     :  0.547   8.598  25428  Z= 0.297
  Chirality :  0.043   0.136   2832
  Planarity :  0.004   0.055   3252
  Dihedral  :  4.223  20.825   2520
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 18.81 %
    Favored  : 77.59 %
  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:  0.04 (0.18), residues: 2208
  helix:  1.16 (0.14), residues: 1488
  sheet: -2.02 (0.37), residues: 120
  loop : -2.44 (0.21), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG L 189 
 TYR   0.030   0.001   TYR K  87 
 PHE   0.018   0.002   PHE H  11 
 TRP   0.012   0.001   TRP K  62 
 HIS   0.008   0.001   HIS G  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (18888)
  covalent geometry    : angle       0.54691 (25428)
  hydrogen bonds       : bond        0.04384 ( 1056)
  hydrogen bonds       : angle       3.97701 ( 3168)

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 229
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   11 PHE cc_start: 0.4577 (OUTLIER) cc_final: 0.4018 (p90)
REVERT: F   20 PHE cc_start: 0.6385 (OUTLIER) cc_final: 0.6155 (m-80)
REVERT: F   51 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7048 (mm-30)
REVERT: D   51 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7487 (mt-10)
REVERT: A   20 PHE cc_start: 0.5131 (OUTLIER) cc_final: 0.4686 (m-80)
REVERT: A   80 THR cc_start: 0.7204 (p) cc_final: 0.6554 (t)
REVERT: B  126 GLU cc_start: 0.4959 (mm-30) cc_final: 0.3938 (pt0)
REVERT: G   51 GLU cc_start: 0.7262 (mm-30) cc_final: 0.7052 (mm-30)
REVERT: J   98 ASN cc_start: 0.7746 (m-40) cc_final: 0.7480 (m-40)
REVERT: I   64 GLU cc_start: 0.6024 (mm-30) cc_final: 0.5601 (mm-30)
REVERT: L   20 PHE cc_start: 0.4765 (OUTLIER) cc_final: 0.4304 (m-80)
REVERT: L   70 LYS cc_start: 0.7298 (mppt) cc_final: 0.7041 (mppt)
REVERT: L  160 ASP cc_start: 0.6381 (t70) cc_final: 0.5795 (m-30)
REVERT: K  180 PHE cc_start: 0.3252 (t80) cc_final: 0.2675 (t80)
  outliers start: 72
  outliers final: 50
  residues processed: 280
  average time/residue: 0.1140
  time to fit residues: 50.2492
Evaluate side-chains
  268 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 213
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    8 THR
Chi-restraints excluded: chain E residue   11 PHE
Chi-restraints excluded: chain E residue   12 THR
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   56 MET
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   20 PHE
Chi-restraints excluded: chain F residue   32 ILE
Chi-restraints excluded: chain F residue   56 MET
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain F residue  183 ILE
Chi-restraints excluded: chain F residue  184 LEU
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  151 GLU
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  175 ILE
Chi-restraints excluded: chain D residue  184 LEU
Chi-restraints excluded: chain A residue    9 SER
Chi-restraints excluded: chain A residue   12 THR
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   73 SER
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain B residue  103 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain H residue   12 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   56 MET
Chi-restraints excluded: chain H residue  183 ILE
Chi-restraints excluded: chain G residue    8 THR
Chi-restraints excluded: chain G residue   32 ILE
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain G residue  106 GLU
Chi-restraints excluded: chain G residue  183 ILE
Chi-restraints excluded: chain G residue  184 LEU
Chi-restraints excluded: chain J residue   67 MET
Chi-restraints excluded: chain J residue  184 LEU
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   32 ILE
Chi-restraints excluded: chain I residue   56 MET
Chi-restraints excluded: chain I residue  175 ILE
Chi-restraints excluded: chain I residue  184 LEU
Chi-restraints excluded: chain L residue   20 PHE
Chi-restraints excluded: chain L residue   50 THR
Chi-restraints excluded: chain L residue  132 LEU
Chi-restraints excluded: chain L residue  175 ILE
Chi-restraints excluded: chain K residue   46 THR
Chi-restraints excluded: chain K residue   73 SER
Chi-restraints excluded: chain K residue  152 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 169 optimal weight:    0.2980
   chunk 110 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 164 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 152 optimal weight:    0.6980
   chunk 109 optimal weight:    0.8980
   chunk 174 optimal weight:    8.9990
   chunk 27 optimal weight:    1.9990
   chunk 124 optimal weight:    0.0980
   chunk 193 optimal weight:   10.0000
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4675 r_free = 0.4675 target = 0.242938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.230805 restraints weight = 22193.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 74)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.212036 restraints weight = 28847.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.210588 restraints weight = 23808.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.210470 restraints weight = 27397.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.210653 restraints weight = 24894.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.4287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6880
moved from start:          0.4384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  18888  Z= 0.110
  Angle     :  0.512   7.680  25428  Z= 0.280
  Chirality :  0.041   0.133   2832
  Planarity :  0.004   0.051   3252
  Dihedral  :  3.974  21.431   2520
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 20.26 %
    Favored  : 76.30 %
  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:  0.13 (0.18), residues: 2208
  helix:  1.20 (0.14), residues: 1488
  sheet: -1.88 (0.36), residues: 120
  loop : -2.33 (0.21), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG L 189 
 TYR   0.025   0.001   TYR K  87 
 PHE   0.023   0.001   PHE D 180 
 TRP   0.010   0.001   TRP C 166 
 HIS   0.009   0.001   HIS G  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (18888)
  covalent geometry    : angle       0.51223 (25428)
  hydrogen bonds       : bond        0.03617 ( 1056)
  hydrogen bonds       : angle       3.87826 ( 3168)

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 227
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
REVERT: E   11 PHE cc_start: 0.4472 (OUTLIER) cc_final: 0.4118 (p90)
REVERT: E   67 MET cc_start: 0.7398 (tmm) cc_final: 0.7025 (tmm)
REVERT: D   51 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7401 (mt-10)
REVERT: D  120 LEU cc_start: 0.6261 (mt) cc_final: 0.6055 (mt)
REVERT: A    1 MET cc_start: 0.5692 (tpp) cc_final: 0.5464 (mmm)
REVERT: A   20 PHE cc_start: 0.5159 (OUTLIER) cc_final: 0.4733 (m-80)
REVERT: A   80 THR cc_start: 0.7156 (p) cc_final: 0.6568 (t)
REVERT: B   11 PHE cc_start: 0.5547 (OUTLIER) cc_final: 0.5203 (p90)
REVERT: B  126 GLU cc_start: 0.4901 (mm-30) cc_final: 0.3774 (pt0)
REVERT: B  180 PHE cc_start: 0.2363 (t80) cc_final: 0.1779 (t80)
REVERT: H   67 MET cc_start: 0.7445 (tmm) cc_final: 0.7084 (tmm)
REVERT: G  133 ARG cc_start: 0.8084 (ttm-80) cc_final: 0.7695 (mtp85)
REVERT: G  134 GLN cc_start: 0.7863 (tp40) cc_final: 0.7632 (tt0)
REVERT: J   98 ASN cc_start: 0.7694 (m-40) cc_final: 0.7449 (m-40)
REVERT: L   70 LYS cc_start: 0.7277 (mppt) cc_final: 0.7077 (mppt)
REVERT: L  160 ASP cc_start: 0.6269 (t70) cc_final: 0.5711 (m-30)
REVERT: K   88 GLU cc_start: 0.4635 (pt0) cc_final: 0.4406 (mm-30)
REVERT: K  180 PHE cc_start: 0.3174 (t80) cc_final: 0.2591 (t80)
  outliers start: 69
  outliers final: 46
  residues processed: 276
  average time/residue: 0.1259
  time to fit residues: 54.5082
Evaluate side-chains
  260 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 210
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    8 THR
Chi-restraints excluded: chain E residue   11 PHE
Chi-restraints excluded: chain E residue   12 THR
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   28 MET
Chi-restraints excluded: chain E residue   56 MET
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   56 MET
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain F residue  175 ILE
Chi-restraints excluded: chain F residue  183 ILE
Chi-restraints excluded: chain F residue  184 LEU
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  184 LEU
Chi-restraints excluded: chain A residue   12 THR
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   11 PHE
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   73 SER
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain H residue   12 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   56 MET
Chi-restraints excluded: chain H residue  183 ILE
Chi-restraints excluded: chain G residue    8 THR
Chi-restraints excluded: chain G residue   32 ILE
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain G residue  106 GLU
Chi-restraints excluded: chain G residue  175 ILE
Chi-restraints excluded: chain G residue  183 ILE
Chi-restraints excluded: chain G residue  184 LEU
Chi-restraints excluded: chain J residue   67 MET
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   32 ILE
Chi-restraints excluded: chain I residue   56 MET
Chi-restraints excluded: chain I residue  106 GLU
Chi-restraints excluded: chain I residue  175 ILE
Chi-restraints excluded: chain I residue  184 LEU
Chi-restraints excluded: chain L residue  132 LEU
Chi-restraints excluded: chain K residue   46 THR
Chi-restraints excluded: chain K residue   73 SER
Chi-restraints excluded: chain K residue  152 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 76 optimal weight:   10.0000
   chunk 171 optimal weight:    3.9990
   chunk 155 optimal weight:    0.0870
   chunk 24 optimal weight:    0.9980
   chunk 116 optimal weight:    1.9990
   chunk 66 optimal weight:    8.9990
   chunk 148 optimal weight:    3.9990
   chunk 85 optimal weight:   20.0000
   chunk 74 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 122 optimal weight:    0.5980
   overall best weight:    1.1362

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

Flipped N/Q/H residues before XYZ refinement:
** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 179 ASN
** L 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4648 r_free = 0.4648 target = 0.239739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.226555 restraints weight = 21875.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.207161 restraints weight = 33259.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.205851 restraints weight = 27852.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.205203 restraints weight = 32452.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.205849 restraints weight = 27753.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.4239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6966
moved from start:          0.4439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  18888  Z= 0.131
  Angle     :  0.539   7.487  25428  Z= 0.292
  Chirality :  0.042   0.133   2832
  Planarity :  0.004   0.046   3252
  Dihedral  :  4.124  21.814   2520
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 20.76 %
    Favored  : 75.90 %
  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:  0.11 (0.18), residues: 2208
  helix:  1.17 (0.14), residues: 1488
  sheet: -1.98 (0.36), residues: 120
  loop : -2.27 (0.21), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG L 189 
 TYR   0.023   0.001   TYR K  87 
 PHE   0.014   0.001   PHE J  11 
 TRP   0.017   0.001   TRP K  62 
 HIS   0.009   0.001   HIS F  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (18888)
  covalent geometry    : angle       0.53860 (25428)
  hydrogen bonds       : bond        0.04081 ( 1056)
  hydrogen bonds       : angle       3.93960 ( 3168)

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 218
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
REVERT: E   11 PHE cc_start: 0.4503 (OUTLIER) cc_final: 0.3968 (p90)
REVERT: E  106 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6963 (mt-10)
REVERT: F   51 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7123 (mm-30)
REVERT: D   51 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7275 (mt-10)
REVERT: A   20 PHE cc_start: 0.5089 (OUTLIER) cc_final: 0.4768 (m-80)
REVERT: A   28 MET cc_start: 0.4171 (tpp) cc_final: 0.3399 (mmm)
REVERT: A   80 THR cc_start: 0.7081 (p) cc_final: 0.6505 (t)
REVERT: B   11 PHE cc_start: 0.5616 (OUTLIER) cc_final: 0.5150 (p90)
REVERT: J   98 ASN cc_start: 0.7749 (m-40) cc_final: 0.7504 (m-40)
REVERT: L   20 PHE cc_start: 0.4923 (OUTLIER) cc_final: 0.4465 (m-80)
REVERT: L  160 ASP cc_start: 0.6403 (t70) cc_final: 0.5823 (m-30)
REVERT: K  180 PHE cc_start: 0.3190 (t80) cc_final: 0.2637 (t80)
  outliers start: 67
  outliers final: 48
  residues processed: 267
  average time/residue: 0.1154
  time to fit residues: 49.1643
Evaluate side-chains
  260 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 207
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    8 THR
Chi-restraints excluded: chain E residue   11 PHE
Chi-restraints excluded: chain E residue   12 THR
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   28 MET
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   56 MET
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   32 ILE
Chi-restraints excluded: chain F residue   56 MET
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain F residue  175 ILE
Chi-restraints excluded: chain F residue  184 LEU
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  181 LYS
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  175 ILE
Chi-restraints excluded: chain D residue  184 LEU
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain B residue   11 PHE
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   73 SER
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain H residue   12 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   56 MET
Chi-restraints excluded: chain H residue  117 VAL
Chi-restraints excluded: chain H residue  183 ILE
Chi-restraints excluded: chain G residue    8 THR
Chi-restraints excluded: chain G residue   32 ILE
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain G residue  106 GLU
Chi-restraints excluded: chain G residue  184 LEU
Chi-restraints excluded: chain J residue   50 THR
Chi-restraints excluded: chain J residue   67 MET
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   32 ILE
Chi-restraints excluded: chain I residue   56 MET
Chi-restraints excluded: chain I residue  106 GLU
Chi-restraints excluded: chain I residue  175 ILE
Chi-restraints excluded: chain I residue  184 LEU
Chi-restraints excluded: chain L residue   20 PHE
Chi-restraints excluded: chain L residue  132 LEU
Chi-restraints excluded: chain K residue   46 THR
Chi-restraints excluded: chain K residue   73 SER
Chi-restraints excluded: chain K residue  103 ILE
Chi-restraints excluded: chain K residue  152 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 157 optimal weight:    5.9990
   chunk 46 optimal weight:    7.9990
   chunk 176 optimal weight:    0.8980
   chunk 71 optimal weight:    4.9990
   chunk 182 optimal weight:    7.9990
   chunk 120 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9990
   chunk 193 optimal weight:    9.9990
   chunk 41 optimal weight:    6.9990
   chunk 170 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.231864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.217049 restraints weight = 22014.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.198163 restraints weight = 31769.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.196426 restraints weight = 25535.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.196352 restraints weight = 30551.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.196726 restraints weight = 27923.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.4149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
moved from start:          0.4575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  18888  Z= 0.223
  Angle     :  0.666   9.525  25428  Z= 0.358
  Chirality :  0.046   0.162   2832
  Planarity :  0.005   0.049   3252
  Dihedral  :  4.787  23.839   2520
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 21.31 %
    Favored  : 75.05 %
  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: -0.29 (0.17), residues: 2208
  helix:  0.85 (0.13), residues: 1488
  sheet: -2.33 (0.35), residues: 120
  loop : -2.35 (0.22), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L 189 
 TYR   0.025   0.002   TYR K  87 
 PHE   0.032   0.002   PHE I 180 
 TRP   0.024   0.002   TRP L 166 
 HIS   0.009   0.001   HIS F  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 (18888)
  covalent geometry    : angle       0.66578 (25428)
  hydrogen bonds       : bond        0.05666 ( 1056)
  hydrogen bonds       : angle       4.34584 ( 3168)

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 219
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
REVERT: E   11 PHE cc_start: 0.4677 (OUTLIER) cc_final: 0.4066 (p90)
REVERT: D   51 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6890 (mp0)
REVERT: A    1 MET cc_start: 0.6231 (mmm) cc_final: 0.5796 (tpt)
REVERT: A   20 PHE cc_start: 0.5000 (OUTLIER) cc_final: 0.4717 (m-80)
REVERT: A   28 MET cc_start: 0.4342 (tpp) cc_final: 0.3662 (mmm)
REVERT: B   11 PHE cc_start: 0.5963 (OUTLIER) cc_final: 0.5368 (p90)
REVERT: J   98 ASN cc_start: 0.7832 (m-40) cc_final: 0.7615 (m-40)
REVERT: I    1 MET cc_start: 0.1039 (tpt) cc_final: 0.0830 (tpt)
REVERT: L   20 PHE cc_start: 0.4891 (OUTLIER) cc_final: 0.4506 (m-80)
REVERT: L  160 ASP cc_start: 0.6726 (t70) cc_final: 0.6103 (m-30)
REVERT: K   11 PHE cc_start: 0.5857 (OUTLIER) cc_final: 0.5403 (p90)
  outliers start: 73
  outliers final: 52
  residues processed: 271
  average time/residue: 0.1210
  time to fit residues: 52.5896
Evaluate side-chains
  256 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 198
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    8 THR
Chi-restraints excluded: chain E residue   11 PHE
Chi-restraints excluded: chain E residue   12 THR
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   56 MET
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   32 ILE
Chi-restraints excluded: chain F residue   56 MET
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain F residue  183 ILE
Chi-restraints excluded: chain F residue  184 LEU
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  151 GLU
Chi-restraints excluded: chain C residue  181 LYS
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  175 ILE
Chi-restraints excluded: chain D residue  184 LEU
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain B residue   11 PHE
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   73 SER
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain B residue  103 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain H residue    8 THR
Chi-restraints excluded: chain H residue   12 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   33 HIS
Chi-restraints excluded: chain H residue  117 VAL
Chi-restraints excluded: chain H residue  183 ILE
Chi-restraints excluded: chain G residue    8 THR
Chi-restraints excluded: chain G residue   32 ILE
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain G residue  106 GLU
Chi-restraints excluded: chain G residue  158 SER
Chi-restraints excluded: chain G residue  184 LEU
Chi-restraints excluded: chain J residue    8 THR
Chi-restraints excluded: chain J residue   50 THR
Chi-restraints excluded: chain J residue   67 MET
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   32 ILE
Chi-restraints excluded: chain I residue  106 GLU
Chi-restraints excluded: chain I residue  175 ILE
Chi-restraints excluded: chain I residue  184 LEU
Chi-restraints excluded: chain L residue   20 PHE
Chi-restraints excluded: chain L residue  132 LEU
Chi-restraints excluded: chain K residue   11 PHE
Chi-restraints excluded: chain K residue   46 THR
Chi-restraints excluded: chain K residue   73 SER
Chi-restraints excluded: chain K residue  103 ILE
Chi-restraints excluded: chain K residue  152 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 187 optimal weight:   10.0000
   chunk 43 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0030
   chunk 159 optimal weight:    0.9990
   chunk 144 optimal weight:    0.6980
   chunk 78 optimal weight:    5.9990
   chunk 108 optimal weight:    0.0470
   chunk 69 optimal weight:    3.9990
   chunk 129 optimal weight:    6.9990
   chunk 83 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.7492

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

Flipped N/Q/H residues before XYZ refinement:
** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4648 r_free = 0.4648 target = 0.239733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.227477 restraints weight = 21803.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 77)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.208718 restraints weight = 30883.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.207034 restraints weight = 26507.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.207132 restraints weight = 28886.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.207625 restraints weight = 26205.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.4262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6944
moved from start:          0.4703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  18888  Z= 0.122
  Angle     :  0.554   9.980  25428  Z= 0.301
  Chirality :  0.042   0.157   2832
  Planarity :  0.004   0.047   3252
  Dihedral  :  4.256  24.299   2520
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 21.86 %
    Favored  : 75.35 %
  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: -0.00 (0.18), residues: 2208
  helix:  1.08 (0.14), residues: 1488
  sheet: -2.20 (0.34), residues: 120
  loop : -2.25 (0.21), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L 189 
 TYR   0.021   0.001   TYR B  87 
 PHE   0.031   0.001   PHE I 180 
 TRP   0.021   0.002   TRP L 166 
 HIS   0.010   0.001   HIS G  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (18888)
  covalent geometry    : angle       0.55389 (25428)
  hydrogen bonds       : bond        0.04041 ( 1056)
  hydrogen bonds       : angle       4.06789 ( 3168)

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 213
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
REVERT: E   11 PHE cc_start: 0.4577 (OUTLIER) cc_final: 0.4359 (p90)
REVERT: E   67 MET cc_start: 0.7369 (tmm) cc_final: 0.6985 (tmm)
REVERT: F  134 GLN cc_start: 0.7919 (tp40) cc_final: 0.7626 (tt0)
REVERT: D   51 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6869 (mp0)
REVERT: A    1 MET cc_start: 0.6274 (mmm) cc_final: 0.5452 (tpt)
REVERT: A   20 PHE cc_start: 0.5000 (OUTLIER) cc_final: 0.4721 (m-80)
REVERT: A   28 MET cc_start: 0.3925 (tpp) cc_final: 0.3248 (mmm)
REVERT: A   70 LYS cc_start: 0.6657 (mmtm) cc_final: 0.6329 (mmtm)
REVERT: B   11 PHE cc_start: 0.5550 (OUTLIER) cc_final: 0.5268 (p90)
REVERT: B   67 MET cc_start: 0.6962 (tmm) cc_final: 0.6505 (ttp)
REVERT: J   98 ASN cc_start: 0.7794 (m-40) cc_final: 0.7587 (m-40)
REVERT: I    1 MET cc_start: 0.0711 (tpt) cc_final: 0.0487 (tpt)
REVERT: L   20 PHE cc_start: 0.4884 (OUTLIER) cc_final: 0.4534 (m-80)
REVERT: L  160 ASP cc_start: 0.6631 (t70) cc_final: 0.6086 (m-30)
REVERT: K   11 PHE cc_start: 0.5439 (OUTLIER) cc_final: 0.5080 (p90)
REVERT: K  180 PHE cc_start: 0.3092 (t80) cc_final: 0.2407 (t80)
  outliers start: 56
  outliers final: 44
  residues processed: 255
  average time/residue: 0.1180
  time to fit residues: 48.2224
Evaluate side-chains
  255 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 205
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    8 THR
Chi-restraints excluded: chain E residue   11 PHE
Chi-restraints excluded: chain E residue   12 THR
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   56 MET
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   32 ILE
Chi-restraints excluded: chain F residue   56 MET
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain F residue  183 ILE
Chi-restraints excluded: chain F residue  184 LEU
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  151 GLU
Chi-restraints excluded: chain C residue  181 LYS
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  175 ILE
Chi-restraints excluded: chain D residue  184 LEU
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain B residue   11 PHE
Chi-restraints excluded: chain B residue   73 SER
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain H residue   12 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   33 HIS
Chi-restraints excluded: chain H residue   56 MET
Chi-restraints excluded: chain H residue  117 VAL
Chi-restraints excluded: chain H residue  183 ILE
Chi-restraints excluded: chain G residue    8 THR
Chi-restraints excluded: chain G residue   32 ILE
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain G residue  106 GLU
Chi-restraints excluded: chain G residue  183 ILE
Chi-restraints excluded: chain G residue  184 LEU
Chi-restraints excluded: chain J residue   67 MET
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue  106 GLU
Chi-restraints excluded: chain I residue  175 ILE
Chi-restraints excluded: chain I residue  184 LEU
Chi-restraints excluded: chain L residue   20 PHE
Chi-restraints excluded: chain L residue  132 LEU
Chi-restraints excluded: chain K residue   11 PHE
Chi-restraints excluded: chain K residue   46 THR
Chi-restraints excluded: chain K residue   73 SER
Chi-restraints excluded: chain K residue  152 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 97 optimal weight:    7.9990
   chunk 207 optimal weight:    9.9990
   chunk 125 optimal weight:    3.9990
   chunk 193 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 202 optimal weight:    0.9980
   chunk 171 optimal weight:    3.9990
   chunk 147 optimal weight:    8.9990
   chunk 41 optimal weight:    1.9990
   chunk 162 optimal weight:    7.9990
   chunk 99 optimal weight:   10.0000
   overall best weight:    2.3986

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

Flipped N/Q/H residues before XYZ refinement:
** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 179 ASN
L 179 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4589 r_free = 0.4589 target = 0.232613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.217730 restraints weight = 21968.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.197619 restraints weight = 31528.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.196626 restraints weight = 26956.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.196428 restraints weight = 30037.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.196569 restraints weight = 27917.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.4147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.4778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  18888  Z= 0.198
  Angle     :  0.648   9.451  25428  Z= 0.349
  Chirality :  0.045   0.175   2832
  Planarity :  0.004   0.048   3252
  Dihedral  :  4.704  25.265   2520
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 21.66 %
    Favored  : 75.10 %
  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: -0.29 (0.17), residues: 2208
  helix:  0.86 (0.13), residues: 1488
  sheet: -2.48 (0.33), residues: 120
  loop : -2.32 (0.22), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H 129 
 TYR   0.021   0.002   TYR B  87 
 PHE   0.022   0.002   PHE H  31 
 TRP   0.022   0.002   TRP L 166 
 HIS   0.009   0.001   HIS F  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 (18888)
  covalent geometry    : angle       0.64788 (25428)
  hydrogen bonds       : bond        0.05293 ( 1056)
  hydrogen bonds       : angle       4.27117 ( 3168)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2709.27 seconds
wall clock time: 48 minutes 13.63 seconds (2893.63 seconds total)