Starting phenix.real_space_refine
on Thu Feb  5 15:04:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jpt_61714/02_2026/9jpt_61714.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jpt_61714/02_2026/9jpt_61714.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jpt_61714/02_2026/9jpt_61714.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jpt_61714/02_2026/9jpt_61714.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jpt_61714/02_2026/9jpt_61714.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jpt_61714/02_2026/9jpt_61714.map"
  }
  resolution = 3.4
  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=   0.021 sd=   0.074
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      96      5.16       5
     C   11352      2.51       5
     N    3064      2.21       5
     O    3448      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 96 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17960
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 2245
          Classifications: {'peptide': 279}
          Link IDs: {'PTRANS': 11, 'TRANS': 267}
  Restraints were copied for chains:
    B, C, D, E, F, G, H
  Time building chain proxies: 1.63, per 1000 atoms: 0.09
  Number of scatterers: 17960
  At special positions: 0
  Unit cell: (213.53, 75.98, 171.61, 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      96     16.00
     O    3448      8.00
     N    3064      7.00
     C   11352      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 218 " - pdb=" SG  CYS B 218 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 218 " - pdb=" SG  CYS D 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 218 " - pdb=" SG  CYS F 218 " distance=2.02
    Simple disulfide: pdb=" SG  CYS G 218 " - pdb=" SG  CYS H 218 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.48
  Conformation dependent library (CDL) restraints added in 745.2 milliseconds
  

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4272

  Finding SS restraints...
    Secondary structure from input PDB file:
      88 helices and 24 sheets defined
      37.3% alpha, 11.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 21
      removed outlier: 4.098A  pdb=" N   SER A  21 " --> pdb=" O   VAL A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 40
    Processing helix  chain 'A' and resid 48 through 55
    Processing helix  chain 'A' and resid 87 through 90
      removed outlier: 4.107A  pdb=" N   GLU A  90 " --> pdb=" O   GLU A  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 87 through 90'
    Processing helix  chain 'A' and resid 99 through 105
    Processing helix  chain 'A' and resid 110 through 122
    Processing helix  chain 'A' and resid 123 through 139
      removed outlier: 3.833A  pdb=" N   GLN A 127 " --> pdb=" O   ASN A 123 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   MET A 136 " --> pdb=" O   GLN A 132 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   TYR A 137 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ARG A 139 " --> pdb=" O   ARG A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 160
      removed outlier: 3.632A  pdb=" N   GLU A 147 " --> pdb=" O   GLU A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 188
      removed outlier: 3.821A  pdb=" N   ASP A 183 " --> pdb=" O   SER A 179 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   VAL A 188 " --> pdb=" O   LEU A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 199
    Processing helix  chain 'A' and resid 267 through 273
      removed outlier: 4.010A  pdb=" N   ARG A 272 " --> pdb=" O   LYS A 269 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   TYR A 273 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 21
      removed outlier: 4.099A  pdb=" N   SER B  21 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 40
    Processing helix  chain 'B' and resid 48 through 55
    Processing helix  chain 'B' and resid 87 through 90
      removed outlier: 4.107A  pdb=" N   GLU B  90 " --> pdb=" O   GLU B  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 87 through 90'
    Processing helix  chain 'B' and resid 99 through 105
    Processing helix  chain 'B' and resid 110 through 122
    Processing helix  chain 'B' and resid 123 through 139
      removed outlier: 3.833A  pdb=" N   GLN B 127 " --> pdb=" O   ASN B 123 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   MET B 136 " --> pdb=" O   GLN B 132 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   TYR B 137 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ARG B 139 " --> pdb=" O   ARG B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 160
      removed outlier: 3.633A  pdb=" N   GLU B 147 " --> pdb=" O   GLU B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 188
      removed outlier: 3.822A  pdb=" N   ASP B 183 " --> pdb=" O   SER B 179 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   VAL B 188 " --> pdb=" O   LEU B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 199
    Processing helix  chain 'B' and resid 267 through 273
      removed outlier: 4.011A  pdb=" N   ARG B 272 " --> pdb=" O   LYS B 269 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   TYR B 273 " --> pdb=" O   LEU B 270 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 21
      removed outlier: 4.099A  pdb=" N   SER C  21 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 36 through 40
    Processing helix  chain 'C' and resid 48 through 55
    Processing helix  chain 'C' and resid 87 through 90
      removed outlier: 4.107A  pdb=" N   GLU C  90 " --> pdb=" O   GLU C  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 87 through 90'
    Processing helix  chain 'C' and resid 99 through 105
    Processing helix  chain 'C' and resid 110 through 122
    Processing helix  chain 'C' and resid 123 through 139
      removed outlier: 3.833A  pdb=" N   GLN C 127 " --> pdb=" O   ASN C 123 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   MET C 136 " --> pdb=" O   GLN C 132 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   TYR C 137 " --> pdb=" O   GLN C 133 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG C 139 " --> pdb=" O   ARG C 135 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 143 through 160
      removed outlier: 3.631A  pdb=" N   GLU C 147 " --> pdb=" O   GLU C 143 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 188
      removed outlier: 3.822A  pdb=" N   ASP C 183 " --> pdb=" O   SER C 179 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   VAL C 188 " --> pdb=" O   LEU C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 199
    Processing helix  chain 'C' and resid 267 through 273
      removed outlier: 4.010A  pdb=" N   ARG C 272 " --> pdb=" O   LYS C 269 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   TYR C 273 " --> pdb=" O   LEU C 270 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 17 through 21
      removed outlier: 4.099A  pdb=" N   SER D  21 " --> pdb=" O   VAL D  18 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 36 through 40
    Processing helix  chain 'D' and resid 48 through 55
    Processing helix  chain 'D' and resid 87 through 90
      removed outlier: 4.106A  pdb=" N   GLU D  90 " --> pdb=" O   GLU D  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 87 through 90'
    Processing helix  chain 'D' and resid 99 through 105
    Processing helix  chain 'D' and resid 110 through 122
    Processing helix  chain 'D' and resid 123 through 139
      removed outlier: 3.834A  pdb=" N   GLN D 127 " --> pdb=" O   ASN D 123 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   MET D 136 " --> pdb=" O   GLN D 132 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   TYR D 137 " --> pdb=" O   GLN D 133 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG D 139 " --> pdb=" O   ARG D 135 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 143 through 160
      removed outlier: 3.631A  pdb=" N   GLU D 147 " --> pdb=" O   GLU D 143 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 179 through 188
      removed outlier: 3.821A  pdb=" N   ASP D 183 " --> pdb=" O   SER D 179 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   VAL D 188 " --> pdb=" O   LEU D 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 199
    Processing helix  chain 'D' and resid 267 through 273
      removed outlier: 4.011A  pdb=" N   ARG D 272 " --> pdb=" O   LYS D 269 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   TYR D 273 " --> pdb=" O   LEU D 270 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 17 through 21
      removed outlier: 4.099A  pdb=" N   SER E  21 " --> pdb=" O   VAL E  18 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 36 through 40
    Processing helix  chain 'E' and resid 48 through 55
    Processing helix  chain 'E' and resid 87 through 90
      removed outlier: 4.107A  pdb=" N   GLU E  90 " --> pdb=" O   GLU E  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 87 through 90'
    Processing helix  chain 'E' and resid 99 through 105
    Processing helix  chain 'E' and resid 110 through 122
    Processing helix  chain 'E' and resid 123 through 139
      removed outlier: 3.834A  pdb=" N   GLN E 127 " --> pdb=" O   ASN E 123 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   MET E 136 " --> pdb=" O   GLN E 132 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   TYR E 137 " --> pdb=" O   GLN E 133 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG E 139 " --> pdb=" O   ARG E 135 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 143 through 160
      removed outlier: 3.632A  pdb=" N   GLU E 147 " --> pdb=" O   GLU E 143 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 179 through 188
      removed outlier: 3.821A  pdb=" N   ASP E 183 " --> pdb=" O   SER E 179 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   VAL E 188 " --> pdb=" O   LEU E 184 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 190 through 199
    Processing helix  chain 'E' and resid 267 through 273
      removed outlier: 4.010A  pdb=" N   ARG E 272 " --> pdb=" O   LYS E 269 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   TYR E 273 " --> pdb=" O   LEU E 270 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 17 through 21
      removed outlier: 4.099A  pdb=" N   SER F  21 " --> pdb=" O   VAL F  18 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 36 through 40
    Processing helix  chain 'F' and resid 48 through 55
    Processing helix  chain 'F' and resid 87 through 90
      removed outlier: 4.106A  pdb=" N   GLU F  90 " --> pdb=" O   GLU F  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 87 through 90'
    Processing helix  chain 'F' and resid 99 through 105
    Processing helix  chain 'F' and resid 110 through 122
    Processing helix  chain 'F' and resid 123 through 139
      removed outlier: 3.834A  pdb=" N   GLN F 127 " --> pdb=" O   ASN F 123 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   MET F 136 " --> pdb=" O   GLN F 132 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   TYR F 137 " --> pdb=" O   GLN F 133 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG F 139 " --> pdb=" O   ARG F 135 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 143 through 160
      removed outlier: 3.632A  pdb=" N   GLU F 147 " --> pdb=" O   GLU F 143 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 179 through 188
      removed outlier: 3.822A  pdb=" N   ASP F 183 " --> pdb=" O   SER F 179 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   VAL F 188 " --> pdb=" O   LEU F 184 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 190 through 199
    Processing helix  chain 'F' and resid 267 through 273
      removed outlier: 4.010A  pdb=" N   ARG F 272 " --> pdb=" O   LYS F 269 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   TYR F 273 " --> pdb=" O   LEU F 270 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 21
      removed outlier: 4.099A  pdb=" N   SER G  21 " --> pdb=" O   VAL G  18 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 36 through 40
    Processing helix  chain 'G' and resid 48 through 55
    Processing helix  chain 'G' and resid 87 through 90
      removed outlier: 4.107A  pdb=" N   GLU G  90 " --> pdb=" O   GLU G  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 87 through 90'
    Processing helix  chain 'G' and resid 99 through 105
    Processing helix  chain 'G' and resid 110 through 122
    Processing helix  chain 'G' and resid 123 through 139
      removed outlier: 3.833A  pdb=" N   GLN G 127 " --> pdb=" O   ASN G 123 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   MET G 136 " --> pdb=" O   GLN G 132 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   TYR G 137 " --> pdb=" O   GLN G 133 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG G 139 " --> pdb=" O   ARG G 135 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 143 through 160
      removed outlier: 3.631A  pdb=" N   GLU G 147 " --> pdb=" O   GLU G 143 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 179 through 188
      removed outlier: 3.822A  pdb=" N   ASP G 183 " --> pdb=" O   SER G 179 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   VAL G 188 " --> pdb=" O   LEU G 184 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 190 through 199
    Processing helix  chain 'G' and resid 267 through 273
      removed outlier: 4.009A  pdb=" N   ARG G 272 " --> pdb=" O   LYS G 269 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   TYR G 273 " --> pdb=" O   LEU G 270 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 17 through 21
      removed outlier: 4.099A  pdb=" N   SER H  21 " --> pdb=" O   VAL H  18 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 36 through 40
    Processing helix  chain 'H' and resid 48 through 55
    Processing helix  chain 'H' and resid 87 through 90
      removed outlier: 4.107A  pdb=" N   GLU H  90 " --> pdb=" O   GLU H  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 87 through 90'
    Processing helix  chain 'H' and resid 99 through 105
    Processing helix  chain 'H' and resid 110 through 122
    Processing helix  chain 'H' and resid 123 through 139
      removed outlier: 3.833A  pdb=" N   GLN H 127 " --> pdb=" O   ASN H 123 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   MET H 136 " --> pdb=" O   GLN H 132 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   TYR H 137 " --> pdb=" O   GLN H 133 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG H 139 " --> pdb=" O   ARG H 135 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 143 through 160
      removed outlier: 3.631A  pdb=" N   GLU H 147 " --> pdb=" O   GLU H 143 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 179 through 188
      removed outlier: 3.821A  pdb=" N   ASP H 183 " --> pdb=" O   SER H 179 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   VAL H 188 " --> pdb=" O   LEU H 184 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 190 through 199
    Processing helix  chain 'H' and resid 267 through 273
      removed outlier: 4.010A  pdb=" N   ARG H 272 " --> pdb=" O   LYS H 269 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   TYR H 273 " --> pdb=" O   LEU H 270 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 80
      removed outlier: 8.115A  pdb=" N   TYR B 276 " --> pdb=" O   LYS A  60 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   ALA A  62 " --> pdb=" O   TYR B 276 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 95
    Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 175
      removed outlier: 6.712A  pdb=" N   SER A 205 " --> pdb=" O   GLN A 287 " (cutoff:3.500A)
      removed outlier: 7.290A  pdb=" N   ILE A 289 " --> pdb=" O   SER A 205 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   THR A 207 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 275 through 277
      removed outlier: 3.775A  pdb=" N   ALA B  64 " --> pdb=" O   TYR A 276 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 92 through 95
    Processing sheet with id=AA6, first strand: chain 'B' and resid 172 through 175
      removed outlier: 6.712A  pdb=" N   SER B 205 " --> pdb=" O   GLN B 287 " (cutoff:3.500A)
      removed outlier: 7.290A  pdb=" N   ILE B 289 " --> pdb=" O   SER B 205 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   THR B 207 " --> pdb=" O   ILE B 289 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 75 through 80
      removed outlier: 8.096A  pdb=" N   TYR D 276 " --> pdb=" O   LYS C  60 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   ALA C  62 " --> pdb=" O   TYR D 276 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 92 through 95
    Processing sheet with id=AA9, first strand: chain 'C' and resid 172 through 175
      removed outlier: 6.712A  pdb=" N   SER C 205 " --> pdb=" O   GLN C 287 " (cutoff:3.500A)
      removed outlier: 7.290A  pdb=" N   ILE C 289 " --> pdb=" O   SER C 205 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   THR C 207 " --> pdb=" O   ILE C 289 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 275 through 277
      removed outlier: 3.786A  pdb=" N   ALA D  64 " --> pdb=" O   TYR C 276 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 92 through 95
    Processing sheet with id=AB3, first strand: chain 'D' and resid 172 through 175
      removed outlier: 6.712A  pdb=" N   SER D 205 " --> pdb=" O   GLN D 287 " (cutoff:3.500A)
      removed outlier: 7.290A  pdb=" N   ILE D 289 " --> pdb=" O   SER D 205 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   THR D 207 " --> pdb=" O   ILE D 289 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 75 through 80
      removed outlier: 8.091A  pdb=" N   TYR F 276 " --> pdb=" O   LYS E  60 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ALA E  62 " --> pdb=" O   TYR F 276 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 92 through 95
    Processing sheet with id=AB6, first strand: chain 'E' and resid 172 through 175
      removed outlier: 6.712A  pdb=" N   SER E 205 " --> pdb=" O   GLN E 287 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   ILE E 289 " --> pdb=" O   SER E 205 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   THR E 207 " --> pdb=" O   ILE E 289 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 275 through 277
      removed outlier: 3.771A  pdb=" N   ALA F  64 " --> pdb=" O   TYR E 276 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 92 through 95
    Processing sheet with id=AB9, first strand: chain 'F' and resid 172 through 175
      removed outlier: 6.712A  pdb=" N   SER F 205 " --> pdb=" O   GLN F 287 " (cutoff:3.500A)
      removed outlier: 7.290A  pdb=" N   ILE F 289 " --> pdb=" O   SER F 205 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   THR F 207 " --> pdb=" O   ILE F 289 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'G' and resid 75 through 80
      removed outlier: 8.101A  pdb=" N   TYR H 276 " --> pdb=" O   LYS G  60 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ALA G  62 " --> pdb=" O   TYR H 276 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'G' and resid 92 through 95
    Processing sheet with id=AC3, first strand: chain 'G' and resid 172 through 175
      removed outlier: 6.712A  pdb=" N   SER G 205 " --> pdb=" O   GLN G 287 " (cutoff:3.500A)
      removed outlier: 7.290A  pdb=" N   ILE G 289 " --> pdb=" O   SER G 205 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   THR G 207 " --> pdb=" O   ILE G 289 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'G' and resid 275 through 277
      removed outlier: 3.794A  pdb=" N   ALA H  64 " --> pdb=" O   TYR G 276 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'H' and resid 92 through 95
    Processing sheet with id=AC6, first strand: chain 'H' and resid 172 through 175
      removed outlier: 6.711A  pdb=" N   SER H 205 " --> pdb=" O   GLN H 287 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   ILE H 289 " --> pdb=" O   SER H 205 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   THR H 207 " --> pdb=" O   ILE H 289 " (cutoff:3.500A)

    588 hydrogen bonds defined for protein.
    1524 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.72

  Time building geometry restraints manager: 1.81 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: 6016
        1.34 -     1.46: 3764
        1.46 -     1.58: 8388
        1.58 -     1.69: 0
        1.69 -     1.81: 120
  Bond restraints: 18288
  Sorted by residual:
  bond pdb=" CA  PHE H  27 "
       pdb=" CB  PHE H  27 "
    ideal  model  delta    sigma   weight residual
    1.527  1.544 -0.017 1.30e-02 5.92e+03 1.63e+00
  bond pdb=" CA  PHE B  27 "
       pdb=" CB  PHE B  27 "
    ideal  model  delta    sigma   weight residual
    1.527  1.544 -0.016 1.30e-02 5.92e+03 1.61e+00
  bond pdb=" CA  PHE C  27 "
       pdb=" CB  PHE C  27 "
    ideal  model  delta    sigma   weight residual
    1.527  1.544 -0.016 1.30e-02 5.92e+03 1.57e+00
  bond pdb=" CA  PHE A  27 "
       pdb=" CB  PHE A  27 "
    ideal  model  delta    sigma   weight residual
    1.527  1.544 -0.016 1.30e-02 5.92e+03 1.56e+00
  bond pdb=" CA  PHE F  27 "
       pdb=" CB  PHE F  27 "
    ideal  model  delta    sigma   weight residual
    1.527  1.544 -0.016 1.30e-02 5.92e+03 1.55e+00
  ... (remaining 18283 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 23929
        1.45 -     2.90: 663
        2.90 -     4.35: 168
        4.35 -     5.81: 16
        5.81 -     7.26: 16
  Bond angle restraints: 24792
  Sorted by residual:
  angle pdb=" N   GLY C 227 "
        pdb=" CA  GLY C 227 "
        pdb=" C   GLY C 227 "
      ideal   model   delta    sigma   weight residual
     111.56  115.13   -3.57 1.01e+00 9.80e-01 1.25e+01
  angle pdb=" N   GLY E 227 "
        pdb=" CA  GLY E 227 "
        pdb=" C   GLY E 227 "
      ideal   model   delta    sigma   weight residual
     111.56  115.08   -3.52 1.01e+00 9.80e-01 1.22e+01
  angle pdb=" N   GLY F 227 "
        pdb=" CA  GLY F 227 "
        pdb=" C   GLY F 227 "
      ideal   model   delta    sigma   weight residual
     111.56  115.07   -3.51 1.01e+00 9.80e-01 1.21e+01
  angle pdb=" N   GLY D 227 "
        pdb=" CA  GLY D 227 "
        pdb=" C   GLY D 227 "
      ideal   model   delta    sigma   weight residual
     111.56  115.05   -3.49 1.01e+00 9.80e-01 1.19e+01
  angle pdb=" N   GLY G 227 "
        pdb=" CA  GLY G 227 "
        pdb=" C   GLY G 227 "
      ideal   model   delta    sigma   weight residual
     111.56  115.05   -3.49 1.01e+00 9.80e-01 1.19e+01
  ... (remaining 24787 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 9991
       17.93 -    35.87: 953
       35.87 -    53.80: 144
       53.80 -    71.74: 33
       71.74 -    89.67: 43
  Dihedral angle restraints: 11164
    sinusoidal: 4548
      harmonic: 6616
  Sorted by residual:
  dihedral pdb=" CB  CYS G 218 "
           pdb=" SG  CYS G 218 "
           pdb=" SG  CYS H 218 "
           pdb=" CB  CYS H 218 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -10.54  -75.46     1      1.00e+01 1.00e-02 7.19e+01
  dihedral pdb=" CB  CYS C 218 "
           pdb=" SG  CYS C 218 "
           pdb=" SG  CYS D 218 "
           pdb=" CB  CYS D 218 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -10.66  -75.34     1      1.00e+01 1.00e-02 7.17e+01
  dihedral pdb=" CB  CYS E 218 "
           pdb=" SG  CYS E 218 "
           pdb=" SG  CYS F 218 "
           pdb=" CB  CYS F 218 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -10.83  -75.17     1      1.00e+01 1.00e-02 7.14e+01
  ... (remaining 11161 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1600
       0.031 -    0.061: 819
       0.061 -    0.092: 249
       0.092 -    0.123: 108
       0.123 -    0.153: 8
  Chirality restraints: 2784
  Sorted by residual:
  chirality pdb=" CB  ILE C  92 "
            pdb=" CA  ILE C  92 "
            pdb=" CG1 ILE C  92 "
            pdb=" CG2 ILE C  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.89e-01
  chirality pdb=" CB  ILE B  92 "
            pdb=" CA  ILE B  92 "
            pdb=" CG1 ILE B  92 "
            pdb=" CG2 ILE B  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.68e-01
  chirality pdb=" CB  ILE G  92 "
            pdb=" CA  ILE G  92 "
            pdb=" CG1 ILE G  92 "
            pdb=" CG2 ILE G  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.52e-01
  ... (remaining 2781 not shown)

  Planarity restraints: 3256
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C  23 "   -0.023 5.00e-02 4.00e+02   3.53e-02 2.00e+00
        pdb=" N   PRO C  24 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO C  24 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO C  24 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS F  23 "   -0.023 5.00e-02 4.00e+02   3.53e-02 1.99e+00
        pdb=" N   PRO F  24 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO F  24 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO F  24 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  23 "   -0.023 5.00e-02 4.00e+02   3.52e-02 1.99e+00
        pdb=" N   PRO B  24 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO B  24 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B  24 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 3253 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1336
        2.74 -     3.28: 19438
        3.28 -     3.82: 28986
        3.82 -     4.36: 35110
        4.36 -     4.90: 59495
  Nonbonded interactions: 144365
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 258 "
            pdb=" OG1 THR B  69 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" NH2 ARG F 135 "
            pdb=" O   CYS G 165 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" OG1 THR G  69 "
            pdb=" OE1 GLN H 258 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OG1 THR E  69 "
            pdb=" OE1 GLN F 258 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" OG1 THR C  69 "
            pdb=" OE1 GLN D 258 "
     model   vdw
     2.213 3.040
  ... (remaining 144360 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             18.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.220
  Find NCS groups from input model:        0.150
  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:             0.010
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
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      :  0.002   0.038  18292  Z= 0.125
  Angle     :  0.621   7.258  24800  Z= 0.333
  Chirality :  0.042   0.153   2784
  Planarity :  0.004   0.035   3256
  Dihedral  : 15.162  89.674   6880
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.91 (0.17), residues: 2216
  helix: -0.41 (0.18), residues: 728
  sheet: -1.42 (0.31), residues: 280
  loop : -1.79 (0.16), residues: 1208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  14 
 TYR   0.015   0.001   TYR E 164 
 PHE   0.012   0.001   PHE E 259 
 TRP   0.003   0.001   TRP H  45 
 HIS   0.001   0.000   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (18288)
  covalent geometry    : angle       0.62082 (24792)
  SS BOND              : bond        0.00781 (    4)
  SS BOND              : angle       0.69867 (    8)
  hydrogen bonds       : bond        0.12643 (  588)
  hydrogen bonds       : angle       5.50039 ( 1524)

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

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

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  493 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 493
  time to evaluate  : 0.655 
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: A  127 GLN cc_start: 0.6604 (pm20) cc_final: 0.6396 (tm-30)
REVERT: A  146 GLU cc_start: 0.4839 (mp0) cc_final: 0.4342 (pm20)
REVERT: A  288 ILE cc_start: 0.6911 (mm) cc_final: 0.6690 (mm)
REVERT: C  119 MET cc_start: 0.7848 (ppp) cc_final: 0.7625 (ptt)
REVERT: C  207 THR cc_start: 0.7739 (m) cc_final: 0.7406 (p)
REVERT: C  244 TYR cc_start: 0.6379 (t80) cc_final: 0.6169 (t80)
REVERT: F   67 ASP cc_start: 0.1485 (p0) cc_final: 0.1274 (p0)
REVERT: F  119 MET cc_start: 0.7782 (ppp) cc_final: 0.7449 (ptt)
REVERT: F  122 ASP cc_start: 0.6318 (t70) cc_final: 0.5942 (t70)
REVERT: F  197 ILE cc_start: 0.8666 (mt) cc_final: 0.8466 (mt)
REVERT: F  200 CYS cc_start: 0.6068 (p) cc_final: 0.5771 (p)
REVERT: G   33 SER cc_start: 0.6209 (p) cc_final: 0.5911 (p)
REVERT: G  164 TYR cc_start: 0.7036 (t80) cc_final: 0.6580 (t80)
REVERT: G  207 THR cc_start: 0.6687 (m) cc_final: 0.6358 (p)
REVERT: H  100 TYR cc_start: 0.7896 (p90) cc_final: 0.7424 (p90)
REVERT: H  136 MET cc_start: 0.5682 (mpp) cc_final: 0.5464 (mpp)
REVERT: H  224 THR cc_start: 0.6780 (p) cc_final: 0.6183 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 493
  average time/residue: 0.1459
  time to fit residues: 102.9098
Evaluate side-chains
  317 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 317
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 194 optimal weight:    0.5980
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    0.0980
   chunk 200 optimal weight:    0.8980
   chunk 212 optimal weight:    0.9990
   chunk 77 optimal weight:    0.0060
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
A 268 GLN
** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 123 ASN
H 127 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.186896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.158363 restraints weight = 27895.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3969 rms_B_bonded: 3.01
r_work: 0.3826 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  18292  Z= 0.124
  Angle     :  0.611   7.954  24800  Z= 0.316
  Chirality :  0.042   0.139   2784
  Planarity :  0.004   0.040   3256
  Dihedral  :  4.974  27.002   2480
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  9.49 %
    Favored  : 89.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.88 (0.16), residues: 2216
  helix: -0.39 (0.18), residues: 688
  sheet: -1.42 (0.31), residues: 280
  loop : -1.73 (0.16), residues: 1248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G 198 
 TYR   0.014   0.001   TYR F 164 
 PHE   0.024   0.001   PHE A  27 
 TRP   0.006   0.001   TRP H  45 
 HIS   0.002   0.001   HIS D  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (18288)
  covalent geometry    : angle       0.61142 (24792)
  SS BOND              : bond        0.00504 (    4)
  SS BOND              : angle       0.50808 (    8)
  hydrogen bonds       : bond        0.03105 (  588)
  hydrogen bonds       : angle       5.12647 ( 1524)

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

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

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  398 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 375
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
REVERT: B  207 THR cc_start: 0.7443 (m) cc_final: 0.6694 (p)
REVERT: B  239 GLN cc_start: 0.7735 (pp30) cc_final: 0.7496 (pp30)
REVERT: C   90 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7607 (tm-30)
REVERT: C  197 ILE cc_start: 0.8916 (mt) cc_final: 0.8491 (tt)
REVERT: C  200 CYS cc_start: 0.7370 (p) cc_final: 0.6999 (p)
REVERT: C  207 THR cc_start: 0.8187 (m) cc_final: 0.7766 (p)
REVERT: C  244 TYR cc_start: 0.6657 (t80) cc_final: 0.6425 (t80)
REVERT: D  199 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7657 (mtpp)
REVERT: E  199 LYS cc_start: 0.7424 (ttmt) cc_final: 0.6794 (mtpt)
REVERT: F  122 ASP cc_start: 0.6992 (t70) cc_final: 0.6667 (t70)
REVERT: F  200 CYS cc_start: 0.6911 (p) cc_final: 0.6495 (p)
REVERT: G  207 THR cc_start: 0.6956 (m) cc_final: 0.6521 (p)
REVERT: H  119 MET cc_start: 0.8312 (ppp) cc_final: 0.8056 (ptt)
REVERT: H  219 ASN cc_start: 0.8145 (p0) cc_final: 0.7884 (p0)
  outliers start: 23
  outliers final: 17
  residues processed: 387
  average time/residue: 0.1440
  time to fit residues: 80.8403
Evaluate side-chains
  331 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 314
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  173 SER
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  290 SER
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain D residue  173 SER
Chi-restraints excluded: chain E residue   92 ILE
Chi-restraints excluded: chain E residue  156 LEU
Chi-restraints excluded: chain E residue  183 ASP
Chi-restraints excluded: chain F residue   41 VAL
Chi-restraints excluded: chain F residue  183 ASP
Chi-restraints excluded: chain F residue  189 LEU
Chi-restraints excluded: chain G residue  205 SER
Chi-restraints excluded: chain H residue   23 LYS
Chi-restraints excluded: chain H residue  191 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 176 optimal weight:    2.9990
   chunk 144 optimal weight:    2.9990
   chunk 193 optimal weight:    0.6980
   chunk 163 optimal weight:    3.9990
   chunk 195 optimal weight:    0.5980
   chunk 118 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 127 optimal weight:    0.0060
   chunk 187 optimal weight:    0.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 127 GLN
F 123 ASN
F 127 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.182251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.153162 restraints weight = 27944.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3914 rms_B_bonded: 3.03
r_work: 0.3749 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  18292  Z= 0.137
  Angle     :  0.608   7.825  24800  Z= 0.312
  Chirality :  0.042   0.146   2784
  Planarity :  0.004   0.038   3256
  Dihedral  :  4.915  26.807   2480
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 12.85 %
    Favored  : 85.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.01 (0.16), residues: 2216
  helix: -0.74 (0.17), residues: 752
  sheet: -1.47 (0.30), residues: 280
  loop : -1.69 (0.16), residues: 1184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 135 
 TYR   0.014   0.001   TYR E 273 
 PHE   0.025   0.002   PHE H  16 
 TRP   0.009   0.001   TRP D  45 
 HIS   0.002   0.001   HIS D  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (18288)
  covalent geometry    : angle       0.60774 (24792)
  SS BOND              : bond        0.00538 (    4)
  SS BOND              : angle       0.46393 (    8)
  hydrogen bonds       : bond        0.03145 (  588)
  hydrogen bonds       : angle       5.11318 ( 1524)

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

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

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  403 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 365
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.8033 (ppt170)
REVERT: B  239 GLN cc_start: 0.7815 (pp30) cc_final: 0.7597 (pp30)
REVERT: B  280 ILE cc_start: 0.8881 (mm) cc_final: 0.8652 (mm)
REVERT: C   83 ASP cc_start: 0.7459 (m-30) cc_final: 0.7043 (m-30)
REVERT: C   90 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7548 (tm-30)
REVERT: C  197 ILE cc_start: 0.8998 (mt) cc_final: 0.8605 (tt)
REVERT: C  207 THR cc_start: 0.8003 (m) cc_final: 0.7481 (p)
REVERT: D   15 ASN cc_start: 0.4899 (t0) cc_final: 0.4264 (m-40)
REVERT: E  199 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7075 (mtpt)
REVERT: F   15 ASN cc_start: 0.6281 (t0) cc_final: 0.5973 (t0)
REVERT: F   79 LYS cc_start: 0.9016 (tttt) cc_final: 0.8740 (ptmt)
REVERT: F   87 GLU cc_start: 0.6560 (mm-30) cc_final: 0.5915 (mm-30)
REVERT: F  127 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7542 (pt0)
REVERT: F  198 ARG cc_start: 0.8271 (mtm110) cc_final: 0.7999 (mtm110)
REVERT: F  200 CYS cc_start: 0.7212 (p) cc_final: 0.6798 (p)
REVERT: G   99 ASN cc_start: 0.7204 (p0) cc_final: 0.6419 (p0)
REVERT: G  162 ASP cc_start: 0.7452 (p0) cc_final: 0.7174 (p0)
REVERT: G  164 TYR cc_start: 0.6981 (t80) cc_final: 0.6573 (t80)
REVERT: H  132 GLN cc_start: 0.8295 (mm-40) cc_final: 0.8059 (mm-40)
REVERT: H  164 TYR cc_start: 0.4145 (t80) cc_final: 0.2853 (m-10)
REVERT: H  224 THR cc_start: 0.6811 (p) cc_final: 0.6366 (p)
REVERT: H  268 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7340 (mp10)
  outliers start: 38
  outliers final: 25
  residues processed: 386
  average time/residue: 0.1420
  time to fit residues: 79.7948
Evaluate side-chains
  342 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 314
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  119 MET
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  154 ARG
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  290 SER
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue  159 THR
Chi-restraints excluded: chain C residue  290 SER
Chi-restraints excluded: chain D residue  105 ASN
Chi-restraints excluded: chain D residue  173 SER
Chi-restraints excluded: chain D residue  266 LEU
Chi-restraints excluded: chain E residue   92 ILE
Chi-restraints excluded: chain E residue  129 GLU
Chi-restraints excluded: chain E residue  156 LEU
Chi-restraints excluded: chain E residue  199 LYS
Chi-restraints excluded: chain E residue  200 CYS
Chi-restraints excluded: chain F residue   33 SER
Chi-restraints excluded: chain F residue   41 VAL
Chi-restraints excluded: chain F residue  127 GLN
Chi-restraints excluded: chain F residue  189 LEU
Chi-restraints excluded: chain G residue  205 SER
Chi-restraints excluded: chain H residue   23 LYS
Chi-restraints excluded: chain H residue  107 SER
Chi-restraints excluded: chain H residue  191 THR
Chi-restraints excluded: chain H residue  243 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 142 optimal weight:    0.0470
   chunk 78 optimal weight:    4.9990
   chunk 164 optimal weight:    0.5980
   chunk 152 optimal weight:    4.9990
   chunk 145 optimal weight:    1.9990
   chunk 178 optimal weight:    1.9990
   chunk 140 optimal weight:    0.0770
   chunk 199 optimal weight:    0.5980
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 127 GLN
F 123 ASN
** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 252 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.180130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.150831 restraints weight = 27736.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3883 rms_B_bonded: 3.04
r_work: 0.3731 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.3281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  18292  Z= 0.140
  Angle     :  0.614   7.821  24800  Z= 0.313
  Chirality :  0.042   0.151   2784
  Planarity :  0.004   0.044   3256
  Dihedral  :  4.923  26.768   2480
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 15.96 %
    Favored  : 82.21 %
  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: -2.06 (0.16), residues: 2216
  helix: -0.80 (0.17), residues: 752
  sheet: -1.54 (0.29), residues: 280
  loop : -1.69 (0.16), residues: 1184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H 198 
 TYR   0.018   0.001   TYR H 118 
 PHE   0.026   0.002   PHE H  16 
 TRP   0.005   0.001   TRP D  45 
 HIS   0.001   0.001   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (18288)
  covalent geometry    : angle       0.61431 (24792)
  SS BOND              : bond        0.00618 (    4)
  SS BOND              : angle       0.51795 (    8)
  hydrogen bonds       : bond        0.03111 (  588)
  hydrogen bonds       : angle       5.11771 ( 1524)

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

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

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  391 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 354
  time to evaluate  : 0.647 
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: A   99 ASN cc_start: 0.7785 (p0) cc_final: 0.7558 (p0)
REVERT: A  154 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.8023 (ppt170)
REVERT: A  183 ASP cc_start: 0.6557 (OUTLIER) cc_final: 0.5995 (m-30)
REVERT: B  239 GLN cc_start: 0.7849 (pp30) cc_final: 0.7644 (pp30)
REVERT: C   90 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7428 (tm-30)
REVERT: C  207 THR cc_start: 0.8005 (m) cc_final: 0.7442 (p)
REVERT: D   15 ASN cc_start: 0.4972 (t0) cc_final: 0.4426 (m-40)
REVERT: E  199 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.6902 (mtpt)
REVERT: F   15 ASN cc_start: 0.6622 (t0) cc_final: 0.6324 (t0)
REVERT: F  129 GLU cc_start: 0.8646 (tt0) cc_final: 0.7953 (tm-30)
REVERT: F  200 CYS cc_start: 0.7309 (p) cc_final: 0.6890 (p)
REVERT: G   99 ASN cc_start: 0.7534 (p0) cc_final: 0.6775 (p0)
REVERT: G  162 ASP cc_start: 0.7447 (p0) cc_final: 0.7107 (p0)
REVERT: G  164 TYR cc_start: 0.6930 (t80) cc_final: 0.6508 (t80)
REVERT: H  164 TYR cc_start: 0.4319 (t80) cc_final: 0.2745 (m-10)
REVERT: H  268 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7373 (mp10)
  outliers start: 37
  outliers final: 26
  residues processed: 375
  average time/residue: 0.1467
  time to fit residues: 80.1343
Evaluate side-chains
  349 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 320
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  154 ARG
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue  159 THR
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue  173 SER
Chi-restraints excluded: chain D residue  266 LEU
Chi-restraints excluded: chain E residue   92 ILE
Chi-restraints excluded: chain E residue  129 GLU
Chi-restraints excluded: chain E residue  156 LEU
Chi-restraints excluded: chain E residue  199 LYS
Chi-restraints excluded: chain E residue  200 CYS
Chi-restraints excluded: chain F residue   33 SER
Chi-restraints excluded: chain F residue   41 VAL
Chi-restraints excluded: chain F residue  229 LEU
Chi-restraints excluded: chain F residue  290 SER
Chi-restraints excluded: chain G residue  200 CYS
Chi-restraints excluded: chain G residue  205 SER
Chi-restraints excluded: chain H residue   23 LYS
Chi-restraints excluded: chain H residue   27 PHE
Chi-restraints excluded: chain H residue  191 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 150 optimal weight:    4.9990
   chunk 135 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9990
   chunk 75 optimal weight:    0.0170
   chunk 214 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 195 optimal weight:    1.9990
   chunk 196 optimal weight:    2.9990
   chunk 189 optimal weight:    2.9990
   chunk 179 optimal weight:    2.9990
   overall best weight:    1.6026

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

Flipped N/Q/H residues before XYZ refinement:
** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 255 ASN
** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 105 ASN
C 258 GLN
** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 127 GLN
G 133 GLN
** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 252 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.169949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.140219 restraints weight = 27468.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 3.00
r_work: 0.3596 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.4478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  18292  Z= 0.266
  Angle     :  0.749   8.767  24800  Z= 0.387
  Chirality :  0.046   0.167   2784
  Planarity :  0.004   0.043   3256
  Dihedral  :  5.484  32.130   2480
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 13.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 17.34 %
    Favored  : 79.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -2.45 (0.15), residues: 2216
  helix: -1.25 (0.16), residues: 752
  sheet: -1.87 (0.28), residues: 280
  loop : -1.79 (0.16), residues: 1184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H 198 
 TYR   0.033   0.002   TYR A 273 
 PHE   0.031   0.003   PHE G  27 
 TRP   0.011   0.002   TRP C  45 
 HIS   0.002   0.001   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00629 (18288)
  covalent geometry    : angle       0.74908 (24792)
  SS BOND              : bond        0.00968 (    4)
  SS BOND              : angle       0.62738 (    8)
  hydrogen bonds       : bond        0.04010 (  588)
  hydrogen bonds       : angle       5.77210 ( 1524)

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

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

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  426 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 364
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.8066 (ppt170)
REVERT: B  239 GLN cc_start: 0.8116 (pp30) cc_final: 0.7898 (pp30)
REVERT: B  286 LYS cc_start: 0.8088 (mtpp) cc_final: 0.7812 (mtpp)
REVERT: C   90 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7820 (tm-30)
REVERT: C   99 ASN cc_start: 0.8723 (p0) cc_final: 0.8395 (p0)
REVERT: C  127 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8258 (pt0)
REVERT: C  207 THR cc_start: 0.7861 (m) cc_final: 0.7302 (p)
REVERT: D  274 GLU cc_start: 0.7451 (pm20) cc_final: 0.7194 (pm20)
REVERT: E  150 ASN cc_start: 0.7363 (t0) cc_final: 0.7086 (m-40)
REVERT: E  199 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7152 (mtpt)
REVERT: E  255 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7446 (t0)
REVERT: E  286 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7775 (ttmm)
REVERT: F   99 ASN cc_start: 0.8378 (p0) cc_final: 0.8114 (p0)
REVERT: F  126 LYS cc_start: 0.8066 (mmmt) cc_final: 0.7705 (mmmt)
REVERT: F  130 ILE cc_start: 0.8803 (mt) cc_final: 0.8448 (mt)
REVERT: F  269 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7704 (pttt)
REVERT: G  162 ASP cc_start: 0.7652 (p0) cc_final: 0.7174 (p0)
REVERT: H  212 ASP cc_start: 0.8033 (p0) cc_final: 0.7648 (p0)
  outliers start: 62
  outliers final: 35
  residues processed: 404
  average time/residue: 0.1398
  time to fit residues: 82.7523
Evaluate side-chains
  361 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 321
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  154 ARG
Chi-restraints excluded: chain A residue  159 THR
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  290 SER
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue  127 GLN
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   58 MET
Chi-restraints excluded: chain D residue  191 THR
Chi-restraints excluded: chain D residue  208 ILE
Chi-restraints excluded: chain D residue  266 LEU
Chi-restraints excluded: chain E residue   92 ILE
Chi-restraints excluded: chain E residue  129 GLU
Chi-restraints excluded: chain E residue  156 LEU
Chi-restraints excluded: chain E residue  183 ASP
Chi-restraints excluded: chain E residue  199 LYS
Chi-restraints excluded: chain E residue  200 CYS
Chi-restraints excluded: chain E residue  234 LEU
Chi-restraints excluded: chain E residue  255 ASN
Chi-restraints excluded: chain F residue   33 SER
Chi-restraints excluded: chain F residue  229 LEU
Chi-restraints excluded: chain F residue  269 LYS
Chi-restraints excluded: chain F residue  290 SER
Chi-restraints excluded: chain G residue  127 GLN
Chi-restraints excluded: chain G residue  208 ILE
Chi-restraints excluded: chain G residue  234 LEU
Chi-restraints excluded: chain H residue   23 LYS
Chi-restraints excluded: chain H residue   27 PHE
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain H residue  256 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 71 optimal weight:    0.0370
   chunk 172 optimal weight:    0.7980
   chunk 126 optimal weight:    2.9990
   chunk 201 optimal weight:    0.5980
   chunk 85 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 91 optimal weight:    0.5980
   chunk 117 optimal weight:    0.7980
   chunk 129 optimal weight:    2.9990
   chunk 188 optimal weight:    0.7980
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 GLN
** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 123 ASN
** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 252 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.174424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.145299 restraints weight = 27304.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3819 rms_B_bonded: 2.99
r_work: 0.3663 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.4468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  18292  Z= 0.135
  Angle     :  0.646   7.468  24800  Z= 0.330
  Chirality :  0.043   0.166   2784
  Planarity :  0.004   0.039   3256
  Dihedral  :  5.200  28.712   2480
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 19.81 %
    Favored  : 78.16 %
  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: -2.25 (0.16), residues: 2216
  helix: -1.01 (0.17), residues: 752
  sheet: -1.80 (0.28), residues: 280
  loop : -1.71 (0.16), residues: 1184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG H 198 
 TYR   0.013   0.001   TYR B 164 
 PHE   0.023   0.001   PHE C  46 
 TRP   0.004   0.001   TRP D  45 
 HIS   0.002   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (18288)
  covalent geometry    : angle       0.64625 (24792)
  SS BOND              : bond        0.00731 (    4)
  SS BOND              : angle       0.68397 (    8)
  hydrogen bonds       : bond        0.03320 (  588)
  hydrogen bonds       : angle       5.35861 ( 1524)

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

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

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  389 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 348
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 ASN cc_start: 0.8178 (p0) cc_final: 0.7860 (p0)
REVERT: A  154 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.8053 (ppt170)
REVERT: A  183 ASP cc_start: 0.6722 (OUTLIER) cc_final: 0.6131 (m-30)
REVERT: B  239 GLN cc_start: 0.8086 (pp30) cc_final: 0.7803 (pp30)
REVERT: C   90 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7710 (tm-30)
REVERT: C   99 ASN cc_start: 0.8570 (p0) cc_final: 0.8321 (p0)
REVERT: C  207 THR cc_start: 0.7913 (m) cc_final: 0.7412 (p)
REVERT: D  160 ASN cc_start: 0.7108 (t0) cc_final: 0.6891 (t0)
REVERT: D  162 ASP cc_start: 0.7657 (p0) cc_final: 0.6966 (p0)
REVERT: D  173 SER cc_start: 0.6473 (OUTLIER) cc_final: 0.6158 (p)
REVERT: E  150 ASN cc_start: 0.7178 (t0) cc_final: 0.6973 (m110)
REVERT: E  199 LYS cc_start: 0.7713 (ttmt) cc_final: 0.7132 (mtpt)
REVERT: E  286 LYS cc_start: 0.8035 (mtpp) cc_final: 0.7682 (ttmm)
REVERT: F   59 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8147 (mt-10)
REVERT: F  269 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7663 (pttt)
REVERT: G  162 ASP cc_start: 0.7709 (p0) cc_final: 0.7228 (p0)
REVERT: G  164 TYR cc_start: 0.7093 (t80) cc_final: 0.6730 (t80)
REVERT: H   42 ASP cc_start: 0.7503 (t0) cc_final: 0.7193 (m-30)
REVERT: H   69 THR cc_start: 0.6941 (m) cc_final: 0.6682 (p)
REVERT: H  212 ASP cc_start: 0.8058 (p0) cc_final: 0.7707 (p0)
  outliers start: 41
  outliers final: 26
  residues processed: 373
  average time/residue: 0.1459
  time to fit residues: 79.4722
Evaluate side-chains
  342 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 312
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  154 ARG
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  290 SER
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue  173 SER
Chi-restraints excluded: chain D residue  191 THR
Chi-restraints excluded: chain D residue  266 LEU
Chi-restraints excluded: chain E residue   92 ILE
Chi-restraints excluded: chain E residue  129 GLU
Chi-restraints excluded: chain E residue  156 LEU
Chi-restraints excluded: chain E residue  183 ASP
Chi-restraints excluded: chain E residue  189 LEU
Chi-restraints excluded: chain F residue   33 SER
Chi-restraints excluded: chain F residue  229 LEU
Chi-restraints excluded: chain F residue  269 LYS
Chi-restraints excluded: chain F residue  290 SER
Chi-restraints excluded: chain H residue   23 LYS
Chi-restraints excluded: chain H residue   27 PHE
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain H residue  191 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 202 optimal weight:    1.9990
   chunk 154 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 191 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 56 optimal weight:    0.1980
   chunk 135 optimal weight:    3.9990
   chunk 209 optimal weight:    3.9990
   chunk 180 optimal weight:    0.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 252 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.173702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.144514 restraints weight = 27593.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3817 rms_B_bonded: 3.01
r_work: 0.3652 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.4620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  18292  Z= 0.149
  Angle     :  0.663   9.201  24800  Z= 0.338
  Chirality :  0.043   0.154   2784
  Planarity :  0.004   0.043   3256
  Dihedral  :  5.134  28.581   2480
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 20.85 %
    Favored  : 76.73 %
  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: -2.19 (0.16), residues: 2216
  helix: -0.95 (0.17), residues: 744
  sheet: -1.78 (0.28), residues: 280
  loop : -1.68 (0.16), residues: 1192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG H 198 
 TYR   0.014   0.001   TYR A 273 
 PHE   0.029   0.002   PHE C  46 
 TRP   0.014   0.001   TRP D  45 
 HIS   0.002   0.001   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (18288)
  covalent geometry    : angle       0.66318 (24792)
  SS BOND              : bond        0.00680 (    4)
  SS BOND              : angle       0.58661 (    8)
  hydrogen bonds       : bond        0.03335 (  588)
  hydrogen bonds       : angle       5.31681 ( 1524)

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

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

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  380 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 331
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.8089 (ppt170)
REVERT: A  158 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7755 (tp)
REVERT: A  183 ASP cc_start: 0.6698 (OUTLIER) cc_final: 0.6127 (m-30)
REVERT: B  124 LYS cc_start: 0.8055 (mmmt) cc_final: 0.7742 (mmmt)
REVERT: B  132 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7711 (mm-40)
REVERT: B  153 LEU cc_start: 0.8428 (tp) cc_final: 0.8176 (tp)
REVERT: B  239 GLN cc_start: 0.8117 (pp30) cc_final: 0.7834 (pp30)
REVERT: C   90 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7716 (tm-30)
REVERT: C   99 ASN cc_start: 0.8591 (p0) cc_final: 0.8342 (p0)
REVERT: C  207 THR cc_start: 0.7911 (m) cc_final: 0.7436 (p)
REVERT: D  173 SER cc_start: 0.6464 (OUTLIER) cc_final: 0.6166 (p)
REVERT: E  199 LYS cc_start: 0.7637 (ttmt) cc_final: 0.7076 (mtpt)
REVERT: E  255 ASN cc_start: 0.7941 (OUTLIER) cc_final: 0.7335 (t0)
REVERT: F  130 ILE cc_start: 0.8783 (mt) cc_final: 0.8551 (mp)
REVERT: F  269 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7686 (pttt)
REVERT: G  162 ASP cc_start: 0.7766 (p0) cc_final: 0.7328 (p0)
REVERT: G  164 TYR cc_start: 0.6915 (t80) cc_final: 0.6689 (t80)
REVERT: H   69 THR cc_start: 0.6974 (m) cc_final: 0.6727 (p)
REVERT: H  212 ASP cc_start: 0.8106 (p0) cc_final: 0.7745 (p0)
REVERT: H  268 GLN cc_start: 0.7576 (mm-40) cc_final: 0.7331 (mp10)
  outliers start: 49
  outliers final: 32
  residues processed: 365
  average time/residue: 0.1473
  time to fit residues: 78.5730
Evaluate side-chains
  352 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 314
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  123 ASN
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  154 ARG
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  290 SER
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue  173 SER
Chi-restraints excluded: chain D residue  191 THR
Chi-restraints excluded: chain D residue  266 LEU
Chi-restraints excluded: chain E residue   92 ILE
Chi-restraints excluded: chain E residue  129 GLU
Chi-restraints excluded: chain E residue  156 LEU
Chi-restraints excluded: chain E residue  189 LEU
Chi-restraints excluded: chain E residue  234 LEU
Chi-restraints excluded: chain E residue  255 ASN
Chi-restraints excluded: chain F residue   33 SER
Chi-restraints excluded: chain F residue   58 MET
Chi-restraints excluded: chain F residue  229 LEU
Chi-restraints excluded: chain F residue  269 LYS
Chi-restraints excluded: chain F residue  290 SER
Chi-restraints excluded: chain H residue   27 PHE
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain H residue  191 THR
Chi-restraints excluded: chain H residue  256 VAL
Chi-restraints excluded: chain H residue  266 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 91 optimal weight:    0.7980
   chunk 78 optimal weight:    8.9990
   chunk 72 optimal weight:    0.0980
   chunk 38 optimal weight:    0.6980
   chunk 105 optimal weight:    0.9990
   chunk 211 optimal weight:    0.7980
   chunk 193 optimal weight:    0.9990
   chunk 172 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 144 optimal weight:    1.9990
   chunk 137 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
C 258 GLN
** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 252 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.174378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.145331 restraints weight = 27396.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3822 rms_B_bonded: 2.99
r_work: 0.3667 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.4767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  18292  Z= 0.143
  Angle     :  0.667   9.685  24800  Z= 0.339
  Chirality :  0.043   0.139   2784
  Planarity :  0.004   0.048   3256
  Dihedral  :  5.086  27.415   2480
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 21.29 %
    Favored  : 76.43 %
  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: -2.16 (0.16), residues: 2216
  helix: -0.90 (0.17), residues: 744
  sheet: -1.76 (0.28), residues: 280
  loop : -1.68 (0.16), residues: 1192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG H 198 
 TYR   0.019   0.001   TYR B 244 
 PHE   0.027   0.001   PHE C  46 
 TRP   0.009   0.001   TRP D  45 
 HIS   0.002   0.001   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (18288)
  covalent geometry    : angle       0.66713 (24792)
  SS BOND              : bond        0.00639 (    4)
  SS BOND              : angle       0.55306 (    8)
  hydrogen bonds       : bond        0.03253 (  588)
  hydrogen bonds       : angle       5.26096 ( 1524)

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

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

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  376 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 330
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.8060 (ppt170)
REVERT: A  158 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7738 (tp)
REVERT: A  183 ASP cc_start: 0.6554 (OUTLIER) cc_final: 0.6053 (m-30)
REVERT: B  124 LYS cc_start: 0.7986 (mmmt) cc_final: 0.7641 (mmmt)
REVERT: B  239 GLN cc_start: 0.8177 (pp30) cc_final: 0.7884 (pp30)
REVERT: C   83 ASP cc_start: 0.7453 (m-30) cc_final: 0.7170 (m-30)
REVERT: C   90 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7774 (tm-30)
REVERT: C   99 ASN cc_start: 0.8557 (p0) cc_final: 0.8308 (p0)
REVERT: C  207 THR cc_start: 0.7934 (m) cc_final: 0.7445 (p)
REVERT: C  233 ARG cc_start: 0.8258 (mmt-90) cc_final: 0.8028 (mmt90)
REVERT: D  173 SER cc_start: 0.6512 (OUTLIER) cc_final: 0.6225 (p)
REVERT: D  226 GLU cc_start: 0.7558 (pm20) cc_final: 0.7276 (pm20)
REVERT: E   99 ASN cc_start: 0.8390 (p0) cc_final: 0.8158 (p0)
REVERT: E  199 LYS cc_start: 0.7671 (ttmt) cc_final: 0.7200 (mtpt)
REVERT: E  255 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7355 (t0)
REVERT: F  130 ILE cc_start: 0.8772 (mt) cc_final: 0.8541 (mp)
REVERT: F  269 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7677 (pttt)
REVERT: G   67 ASP cc_start: 0.5510 (p0) cc_final: 0.5273 (p0)
REVERT: G  162 ASP cc_start: 0.7197 (p0) cc_final: 0.6987 (p0)
REVERT: G  222 ARG cc_start: 0.7700 (ttm170) cc_final: 0.7212 (ttm-80)
REVERT: H   42 ASP cc_start: 0.7316 (t0) cc_final: 0.7110 (m-30)
REVERT: H  212 ASP cc_start: 0.8045 (p0) cc_final: 0.7672 (p0)
REVERT: H  268 GLN cc_start: 0.7530 (mm-40) cc_final: 0.7124 (pm20)
  outliers start: 46
  outliers final: 35
  residues processed: 361
  average time/residue: 0.1463
  time to fit residues: 77.0265
Evaluate side-chains
  361 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 320
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  123 ASN
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  154 ARG
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  290 SER
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue  173 SER
Chi-restraints excluded: chain D residue  191 THR
Chi-restraints excluded: chain D residue  256 VAL
Chi-restraints excluded: chain D residue  266 LEU
Chi-restraints excluded: chain E residue   92 ILE
Chi-restraints excluded: chain E residue  129 GLU
Chi-restraints excluded: chain E residue  156 LEU
Chi-restraints excluded: chain E residue  189 LEU
Chi-restraints excluded: chain E residue  234 LEU
Chi-restraints excluded: chain E residue  255 ASN
Chi-restraints excluded: chain F residue   33 SER
Chi-restraints excluded: chain F residue   58 MET
Chi-restraints excluded: chain F residue   89 ILE
Chi-restraints excluded: chain F residue  229 LEU
Chi-restraints excluded: chain F residue  269 LYS
Chi-restraints excluded: chain F residue  290 SER
Chi-restraints excluded: chain G residue   27 PHE
Chi-restraints excluded: chain H residue   27 PHE
Chi-restraints excluded: chain H residue   72 ASN
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain H residue  191 THR
Chi-restraints excluded: chain H residue  256 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 77 optimal weight:    0.0470
   chunk 138 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 199 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 75 optimal weight:    0.4980
   chunk 38 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 46 optimal weight:    0.3980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 252 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.175692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.146895 restraints weight = 27211.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3839 rms_B_bonded: 2.98
r_work: 0.3684 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.4808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  18292  Z= 0.130
  Angle     :  0.661   9.122  24800  Z= 0.334
  Chirality :  0.042   0.145   2784
  Planarity :  0.004   0.053   3256
  Dihedral  :  4.981  26.185   2480
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 21.69 %
    Favored  : 76.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.08 (0.16), residues: 2216
  helix: -0.82 (0.17), residues: 744
  sheet: -1.71 (0.29), residues: 280
  loop : -1.65 (0.16), residues: 1192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG H 198 
 TYR   0.024   0.001   TYR G 164 
 PHE   0.020   0.001   PHE C  46 
 TRP   0.010   0.001   TRP D  45 
 HIS   0.001   0.001   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (18288)
  covalent geometry    : angle       0.66068 (24792)
  SS BOND              : bond        0.00578 (    4)
  SS BOND              : angle       0.55195 (    8)
  hydrogen bonds       : bond        0.03162 (  588)
  hydrogen bonds       : angle       5.15585 ( 1524)

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

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

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  374 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 329
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.8026 (ppt170)
REVERT: A  183 ASP cc_start: 0.6798 (m-30) cc_final: 0.6288 (m-30)
REVERT: B  239 GLN cc_start: 0.8174 (pp30) cc_final: 0.7878 (pp30)
REVERT: C   83 ASP cc_start: 0.7357 (m-30) cc_final: 0.7051 (m-30)
REVERT: C   90 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7709 (tm-30)
REVERT: C   99 ASN cc_start: 0.8474 (p0) cc_final: 0.8214 (p0)
REVERT: C  207 THR cc_start: 0.8027 (m) cc_final: 0.7530 (p)
REVERT: E   99 ASN cc_start: 0.8418 (p0) cc_final: 0.8186 (p0)
REVERT: E  199 LYS cc_start: 0.7623 (ttmt) cc_final: 0.7153 (mtpt)
REVERT: E  255 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7340 (t0)
REVERT: F  269 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7621 (pttt)
REVERT: G   67 ASP cc_start: 0.5470 (p0) cc_final: 0.5249 (p0)
REVERT: G  222 ARG cc_start: 0.7682 (ttm170) cc_final: 0.7195 (ttm-80)
REVERT: H  212 ASP cc_start: 0.8056 (p0) cc_final: 0.7682 (p0)
REVERT: H  268 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7129 (pm20)
  outliers start: 45
  outliers final: 35
  residues processed: 361
  average time/residue: 0.1518
  time to fit residues: 80.2994
Evaluate side-chains
  352 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 314
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  123 ASN
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  154 ARG
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  290 SER
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue  125 GLU
Chi-restraints excluded: chain D residue  256 VAL
Chi-restraints excluded: chain D residue  266 LEU
Chi-restraints excluded: chain E residue   92 ILE
Chi-restraints excluded: chain E residue  129 GLU
Chi-restraints excluded: chain E residue  156 LEU
Chi-restraints excluded: chain E residue  255 ASN
Chi-restraints excluded: chain F residue   58 MET
Chi-restraints excluded: chain F residue   89 ILE
Chi-restraints excluded: chain F residue  229 LEU
Chi-restraints excluded: chain F residue  256 VAL
Chi-restraints excluded: chain F residue  269 LYS
Chi-restraints excluded: chain F residue  290 SER
Chi-restraints excluded: chain G residue   27 PHE
Chi-restraints excluded: chain H residue   27 PHE
Chi-restraints excluded: chain H residue   72 ASN
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain H residue  191 THR
Chi-restraints excluded: chain H residue  256 VAL
Chi-restraints excluded: chain H residue  266 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 195 optimal weight:    0.6980
   chunk 121 optimal weight:    0.7980
   chunk 166 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 181 optimal weight:    2.9990
   chunk 190 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 158 optimal weight:    2.9990
   chunk 127 optimal weight:    0.5980
   chunk 116 optimal weight:    0.9980
   chunk 107 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C 258 GLN
** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 252 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.172607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.143771 restraints weight = 27295.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3807 rms_B_bonded: 2.96
r_work: 0.3653 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.5074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  18292  Z= 0.164
  Angle     :  0.691   9.606  24800  Z= 0.351
  Chirality :  0.043   0.158   2784
  Planarity :  0.004   0.054   3256
  Dihedral  :  5.052  26.814   2480
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 22.18 %
    Favored  : 75.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.14 (0.16), residues: 2216
  helix: -0.87 (0.17), residues: 744
  sheet: -1.76 (0.29), residues: 280
  loop : -1.67 (0.16), residues: 1192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG H 198 
 TYR   0.030   0.002   TYR B 244 
 PHE   0.021   0.002   PHE D  27 
 TRP   0.003   0.001   TRP H  45 
 HIS   0.002   0.001   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (18288)
  covalent geometry    : angle       0.69147 (24792)
  SS BOND              : bond        0.00631 (    4)
  SS BOND              : angle       0.46021 (    8)
  hydrogen bonds       : bond        0.03380 (  588)
  hydrogen bonds       : angle       5.27600 ( 1524)

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

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

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  378 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 335
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8064 (ppt170)
REVERT: A  158 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7740 (tp)
REVERT: A  183 ASP cc_start: 0.6564 (m-30) cc_final: 0.6065 (m-30)
REVERT: B  239 GLN cc_start: 0.8132 (pp30) cc_final: 0.7921 (pp30)
REVERT: C   83 ASP cc_start: 0.7565 (m-30) cc_final: 0.7288 (m-30)
REVERT: C   90 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7721 (tm-30)
REVERT: C   99 ASN cc_start: 0.8559 (p0) cc_final: 0.8298 (p0)
REVERT: C  182 ASP cc_start: 0.7687 (m-30) cc_final: 0.7376 (t0)
REVERT: C  207 THR cc_start: 0.7875 (m) cc_final: 0.7413 (p)
REVERT: E   99 ASN cc_start: 0.8524 (p0) cc_final: 0.8287 (p0)
REVERT: E  146 GLU cc_start: 0.3498 (mp0) cc_final: 0.3295 (mp0)
REVERT: E  150 ASN cc_start: 0.7324 (t0) cc_final: 0.7084 (m110)
REVERT: E  162 ASP cc_start: 0.7945 (p0) cc_final: 0.7394 (p0)
REVERT: E  255 ASN cc_start: 0.7936 (OUTLIER) cc_final: 0.7422 (t0)
REVERT: F  130 ILE cc_start: 0.8723 (mt) cc_final: 0.8475 (mp)
REVERT: F  269 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7636 (pttt)
REVERT: G  222 ARG cc_start: 0.7715 (ttm170) cc_final: 0.7224 (ttm-80)
REVERT: H  212 ASP cc_start: 0.8059 (p0) cc_final: 0.7699 (p0)
REVERT: H  268 GLN cc_start: 0.7525 (mm-40) cc_final: 0.7276 (pm20)
  outliers start: 43
  outliers final: 36
  residues processed: 368
  average time/residue: 0.1483
  time to fit residues: 79.9746
Evaluate side-chains
  353 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 313
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  123 ASN
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  154 ARG
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  290 SER
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue  170 THR
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue  191 THR
Chi-restraints excluded: chain D residue  256 VAL
Chi-restraints excluded: chain D residue  266 LEU
Chi-restraints excluded: chain E residue   92 ILE
Chi-restraints excluded: chain E residue  129 GLU
Chi-restraints excluded: chain E residue  156 LEU
Chi-restraints excluded: chain E residue  189 LEU
Chi-restraints excluded: chain E residue  255 ASN
Chi-restraints excluded: chain F residue   58 MET
Chi-restraints excluded: chain F residue  229 LEU
Chi-restraints excluded: chain F residue  256 VAL
Chi-restraints excluded: chain F residue  269 LYS
Chi-restraints excluded: chain G residue   27 PHE
Chi-restraints excluded: chain H residue   27 PHE
Chi-restraints excluded: chain H residue   72 ASN
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain H residue  191 THR
Chi-restraints excluded: chain H residue  256 VAL
Chi-restraints excluded: chain H residue  266 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 146 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 206 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 143 optimal weight:    1.9990
   chunk 203 optimal weight:    0.8980
   chunk 145 optimal weight:    0.6980
   chunk 178 optimal weight:    8.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B 268 GLN
** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 123 ASN
** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 252 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.172229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.143323 restraints weight = 27589.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3800 rms_B_bonded: 2.99
r_work: 0.3648 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.5237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  18292  Z= 0.171
  Angle     :  0.709   9.613  24800  Z= 0.360
  Chirality :  0.043   0.192   2784
  Planarity :  0.004   0.055   3256
  Dihedral  :  5.099  26.945   2480
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 22.48 %
    Favored  : 75.30 %
  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: -2.18 (0.16), residues: 2216
  helix: -0.91 (0.17), residues: 744
  sheet: -1.79 (0.29), residues: 280
  loop : -1.68 (0.16), residues: 1192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG H 198 
 TYR   0.023   0.002   TYR D 244 
 PHE   0.053   0.002   PHE H  16 
 TRP   0.011   0.001   TRP A  45 
 HIS   0.002   0.001   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (18288)
  covalent geometry    : angle       0.70892 (24792)
  SS BOND              : bond        0.00641 (    4)
  SS BOND              : angle       0.48177 (    8)
  hydrogen bonds       : bond        0.03389 (  588)
  hydrogen bonds       : angle       5.32126 ( 1524)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4084.88 seconds
wall clock time: 71 minutes 21.38 seconds (4281.38 seconds total)