Starting phenix.real_space_refine
on Wed Aug  5 19:33:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9tit_55969/08_2026/9tit_55969.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9tit_55969/08_2026/9tit_55969.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9tit_55969/08_2026/9tit_55969.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9tit_55969/08_2026/9tit_55969.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9tit_55969/08_2026/9tit_55969.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9tit_55969/08_2026/9tit_55969.cif"
  }
  resolution = 4.4
  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=   0.000 sd=   0.002
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      20      5.16       5
     C    7107      2.51       5
     N    1815      2.21       5
     O    2255      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11197
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "C"
      Number of atoms: 1145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1145
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 5, 'TRANS': 138}
          Chain breaks: 3
    Chain: "E"
      Number of atoms: 1349
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 1349
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 9, 'TRANS': 162}
    Chain: "G"
      Number of atoms: 2190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 265, 2190
          Classifications: {'peptide': 265}
          Link IDs: {'PTRANS': 6, 'TRANS': 258}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 1295
          Classifications: {'peptide': 165}
          Link IDs: {'PTRANS': 8, 'TRANS': 156}
          Chain breaks: 1
    Chain: "Q"
      Number of atoms: 1237
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1237
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 8, 'TRANS': 148}
          Chain breaks: 1
    Chain: "U"
      Number of atoms: 1327
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 168, 1327
          Classifications: {'peptide': 168}
          Link IDs: {'PTRANS': 8, 'TRANS': 159}
    Chain: "V"
      Number of atoms: 1327
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 168, 1327
          Classifications: {'peptide': 168}
          Link IDs: {'PTRANS': 8, 'TRANS': 159}
    Chain: "W"
      Number of atoms: 1327
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 168, 1327
          Classifications: {'peptide': 168}
          Link IDs: {'PTRANS': 8, 'TRANS': 159}
  Time building chain proxies: 2.60, per 1000 atoms: 0.23
  Number of scatterers: 11197
  At special positions: 0
  Unit cell: (127.897, 128.954, 103.586, 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      20     16.00
     O    2255      8.00
     N    1815      7.00
     C    7107      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 367.5 milliseconds
  

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2640

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 24 sheets defined
      18.4% alpha, 31.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'C' and resid 6 through 19
      removed outlier: 3.653A  pdb=" N   VAL C  10 " --> pdb=" O   TYR C   6 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   GLU C  11 " --> pdb=" O   ASN C   7 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU C  12 " --> pdb=" O   SER C   8 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   LYS C  14 " --> pdb=" O   VAL C  10 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   TYR C  15 " --> pdb=" O   GLU C  11 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   LEU C  16 " --> pdb=" O   LEU C  12 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   VAL C  17 " --> pdb=" O   ALA C  13 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LYS C  19 " --> pdb=" O   TYR C  15 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 22
      No H-bonds generated for 'chain 'C' and resid 20 through 22'
    Processing helix  chain 'C' and resid 89 through 91
      No H-bonds generated for 'chain 'C' and resid 89 through 91'
    Processing helix  chain 'C' and resid 92 through 97
    Processing helix  chain 'C' and resid 138 through 142
    Processing helix  chain 'E' and resid 5 through 19
      removed outlier: 3.989A  pdb=" N   HIS E   9 " --> pdb=" O   THR E   5 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   VAL E  10 " --> pdb=" O   TYR E   6 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU E  12 " --> pdb=" O   SER E   8 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   TYR E  15 " --> pdb=" O   GLU E  11 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU E  16 " --> pdb=" O   LEU E  12 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 22
      No H-bonds generated for 'chain 'E' and resid 20 through 22'
    Processing helix  chain 'E' and resid 69 through 73
    Processing helix  chain 'E' and resid 89 through 91
      No H-bonds generated for 'chain 'E' and resid 89 through 91'
    Processing helix  chain 'E' and resid 92 through 97
    Processing helix  chain 'E' and resid 110 through 112
      No H-bonds generated for 'chain 'E' and resid 110 through 112'
    Processing helix  chain 'E' and resid 138 through 140
      No H-bonds generated for 'chain 'E' and resid 138 through 140'
    Processing helix  chain 'G' and resid 249 through 254
      removed outlier: 3.565A  pdb=" N   VAL G 252 " --> pdb=" O   SER G 249 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 277 through 282
    Processing helix  chain 'G' and resid 290 through 295
    Processing helix  chain 'G' and resid 324 through 332
    Processing helix  chain 'G' and resid 341 through 351
    Processing helix  chain 'H' and resid 7 through 19
      removed outlier: 3.842A  pdb=" N   GLU H  11 " --> pdb=" O   ASN H   7 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 20 through 22
      No H-bonds generated for 'chain 'H' and resid 20 through 22'
    Processing helix  chain 'H' and resid 89 through 97
      removed outlier: 4.554A  pdb=" N   LYS H  94 " --> pdb=" O   PRO H  90 " (cutoff:3.500A)
      removed outlier: 5.184A  pdb=" N   ALA H  95 " --> pdb=" O   GLU H  91 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 138 through 140
      No H-bonds generated for 'chain 'H' and resid 138 through 140'
    Processing helix  chain 'Q' and resid 5 through 8
    Processing helix  chain 'Q' and resid 9 through 19
    Processing helix  chain 'Q' and resid 20 through 22
      No H-bonds generated for 'chain 'Q' and resid 20 through 22'
    Processing helix  chain 'Q' and resid 89 through 91
      No H-bonds generated for 'chain 'Q' and resid 89 through 91'
    Processing helix  chain 'Q' and resid 92 through 97
    Processing helix  chain 'U' and resid 15 through 18
    Processing helix  chain 'U' and resid 32 through 53
      removed outlier: 4.071A  pdb=" N   LEU U  36 " --> pdb=" O   GLN U  32 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASP U  43 " --> pdb=" O   MET U  39 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU U  47 " --> pdb=" O   ASP U  43 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LYS U  48 " --> pdb=" O   GLN U  44 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 120 through 124
    Processing helix  chain 'V' and resid 15 through 18
    Processing helix  chain 'V' and resid 32 through 55
      removed outlier: 3.992A  pdb=" N   LEU V  36 " --> pdb=" O   GLN V  32 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ASN V  37 " --> pdb=" O   GLN V  33 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ASP V  43 " --> pdb=" O   MET V  39 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE V  54 " --> pdb=" O   LEU V  50 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 120 through 124
    Processing helix  chain 'W' and resid 15 through 18
    Processing helix  chain 'W' and resid 32 through 55
      removed outlier: 3.700A  pdb=" N   LEU W  36 " --> pdb=" O   GLN W  32 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 120 through 124
    Processing sheet with id=AA1, first strand: chain 'C' and resid 52 through 57
      removed outlier: 3.575A  pdb=" N   GLY C  54 " --> pdb=" O   ILE C  27 " (cutoff:3.500A)
      removed outlier: 9.425A  pdb=" N   THR C 116 " --> pdb=" O   GLN C 155 " (cutoff:3.500A)
      removed outlier: 10.709A  pdb=" N   GLN C 155 " --> pdb=" O   THR C 116 " (cutoff:3.500A)
      removed outlier: 8.744A  pdb=" N   ARG C 118 " --> pdb=" O   ASN C 153 " (cutoff:3.500A)
      removed outlier: 5.182A  pdb=" N   ASN C 153 " --> pdb=" O   ARG C 118 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   VAL C 120 " --> pdb=" O   PHE C 151 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   PHE C 151 " --> pdb=" O   VAL C 120 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   PHE C 122 " --> pdb=" O   LEU C 149 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 85 through 88
      removed outlier: 3.661A  pdb=" N   THR C  62 " --> pdb=" O   TYR C 102 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   TRP C 100 " --> pdb=" O   VAL C  64 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   VAL C 101 " --> pdb=" O   VAL C 171 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LYS H 166 " --> pdb=" O   PHE G 203 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   SER H 105 " --> pdb=" O   GLU H 167 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   TRP H 100 " --> pdb=" O   VAL H  64 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU H  63 " --> pdb=" O   VAL H  88 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 3 through 4
      removed outlier: 6.626A  pdb=" N   LEU H 148 " --> pdb=" O   MET H 124 " (cutoff:3.500A)
      removed outlier: 7.668A  pdb=" N   MET H 124 " --> pdb=" O   LEU H 148 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   PHE H 150 " --> pdb=" O   PHE H 122 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ILE H  27 " --> pdb=" O   GLY H  54 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   GLY H  54 " --> pdb=" O   ILE H  27 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 136 through 137
      removed outlier: 7.000A  pdb=" N   ILE E  27 " --> pdb=" O   ILE E  53 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   TYR E  55 " --> pdb=" O   LEU E  25 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   LEU E  25 " --> pdb=" O   TYR E  55 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   VAL E 120 " --> pdb=" O   PHE E 151 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   PHE E 151 " --> pdb=" O   VAL E 120 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   PHE E 122 " --> pdb=" O   LEU E 149 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 77 through 80
      removed outlier: 3.982A  pdb=" N   LEU E  63 " --> pdb=" O   VAL E  88 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   LYS E  60 " --> pdb=" O   GLU E 104 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   TRP E 100 " --> pdb=" O   VAL E  64 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 127 through 128
      removed outlier: 6.292A  pdb=" N   VAL E 127 " --> pdb=" O   GLU E 143 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 213 through 217
      removed outlier: 3.627A  pdb=" N   TYR G 442 " --> pdb=" O   PHE G 213 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASN G 434 " --> pdb=" O   TYR G 358 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   TYR G 358 " --> pdb=" O   ASN G 434 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   LEU G 436 " --> pdb=" O   ASP G 356 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   ASP G 356 " --> pdb=" O   LEU G 436 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   LEU G 438 " --> pdb=" O   SER G 354 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   SER G 354 " --> pdb=" O   LEU G 438 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'G' and resid 305 through 310
      removed outlier: 3.586A  pdb=" N   ASN G 434 " --> pdb=" O   TYR G 358 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   TYR G 358 " --> pdb=" O   ASN G 434 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   LEU G 436 " --> pdb=" O   ASP G 356 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   ASP G 356 " --> pdb=" O   LEU G 436 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   LEU G 438 " --> pdb=" O   SER G 354 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   SER G 354 " --> pdb=" O   LEU G 438 " (cutoff:3.500A)
      removed outlier: 5.900A  pdb=" N   LEU G 353 " --> pdb=" O   ILE G 402 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'G' and resid 287 through 288
      removed outlier: 3.710A  pdb=" N   TYR G 259 " --> pdb=" O   ASN G 321 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   PHE G 416 " --> pdb=" O   TYR G 376 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   TYR G 376 " --> pdb=" O   PHE G 416 " (cutoff:3.500A)
      removed outlier: 7.948A  pdb=" N   ILE G 371 " --> pdb=" O   ILE G 388 " (cutoff:3.500A)
      removed outlier: 5.723A  pdb=" N   ILE G 388 " --> pdb=" O   ILE G 371 " (cutoff:3.500A)
      removed outlier: 7.382A  pdb=" N   LEU G 373 " --> pdb=" O   VAL G 386 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'G' and resid 368 through 369
      removed outlier: 3.608A  pdb=" N   LEU G 391 " --> pdb=" O   ILE G 369 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'G' and resid 464 through 467
      removed outlier: 3.579A  pdb=" N   ARG G 465 " --> pdb=" O   LYS Q 166 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ARG Q 168 " --> pdb=" O   ARG G 465 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 127 through 128
      removed outlier: 3.645A  pdb=" N   VAL H 127 " --> pdb=" O   SER H 144 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'Q' and resid 136 through 137
      removed outlier: 3.644A  pdb=" N   TYR Q  24 " --> pdb=" O   VAL Q 123 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   VAL Q 120 " --> pdb=" O   ASP Q 152 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   PHE Q 150 " --> pdb=" O   PHE Q 122 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'Q' and resid 86 through 88
      removed outlier: 4.009A  pdb=" N   LEU Q  63 " --> pdb=" O   VAL Q  88 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   TRP Q 100 " --> pdb=" O   VAL Q  64 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'Q' and resid 127 through 128
      removed outlier: 7.050A  pdb=" N   VAL Q 127 " --> pdb=" O   GLU Q 143 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'U' and resid 20 through 24
      removed outlier: 6.244A  pdb=" N   ARG U  20 " --> pdb=" O   GLU V 143 " (cutoff:3.500A)
      removed outlier: 7.120A  pdb=" N   GLU V 143 " --> pdb=" O   ARG U  20 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   LYS U  22 " --> pdb=" O   LEU V 141 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLY V 107 " --> pdb=" O   THR V 148 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   GLU V 104 " --> pdb=" O   THR V 159 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   THR V 159 " --> pdb=" O   GLU V 104 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ILE V 106 " --> pdb=" O   ILE V 157 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'U' and resid 60 through 63
      removed outlier: 6.791A  pdb=" N   TYR U  80 " --> pdb=" O   GLN U  61 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'U' and resid 66 through 68
    Processing sheet with id=AC1, first strand: chain 'U' and resid 164 through 165
      removed outlier: 6.713A  pdb=" N   ILE U 106 " --> pdb=" O   ILE U 157 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   THR U 159 " --> pdb=" O   GLU U 104 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   GLU U 104 " --> pdb=" O   THR U 159 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   SER U 146 " --> pdb=" O   LYS U 109 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   LYS W  22 " --> pdb=" O   LEU U 141 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   GLU U 143 " --> pdb=" O   ARG W  20 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   ARG W  20 " --> pdb=" O   GLU U 143 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'V' and resid 20 through 24
      removed outlier: 5.950A  pdb=" N   ARG V  20 " --> pdb=" O   GLU W 143 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   GLU W 143 " --> pdb=" O   ARG V  20 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   LYS V  22 " --> pdb=" O   LEU W 141 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LYS W 144 " --> pdb=" O   THR W 111 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLY W 107 " --> pdb=" O   THR W 148 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   GLU W 104 " --> pdb=" O   THR W 159 " (cutoff:3.500A)
      removed outlier: 4.901A  pdb=" N   THR W 159 " --> pdb=" O   GLU W 104 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   ILE W 106 " --> pdb=" O   ILE W 157 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'V' and resid 59 through 63
      removed outlier: 3.513A  pdb=" N   TYR V  82 " --> pdb=" O   ASP V  59 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   TYR V  80 " --> pdb=" O   GLN V  61 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'V' and resid 66 through 68
    Processing sheet with id=AC5, first strand: chain 'W' and resid 59 through 63
      removed outlier: 4.027A  pdb=" N   ASP W  59 " --> pdb=" O   TYR W  82 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLN W  61 " --> pdb=" O   TYR W  80 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   TYR W  80 " --> pdb=" O   GLN W  61 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   VAL W  81 " --> pdb=" O   ARG W  88 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'W' and resid 66 through 68

    359 hydrogen bonds defined for protein.
    912 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.81

  Time building geometry restraints manager: 1.05 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: 3617
        1.34 -     1.46: 2575
        1.46 -     1.58: 5186
        1.58 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 11418
  Sorted by residual:
  bond pdb=" N   ASN V   4 "
       pdb=" CA  ASN V   4 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.11e+00
  bond pdb=" N   ASN U   4 "
       pdb=" CA  ASN U   4 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.01e+00
  bond pdb=" N   ASN W   4 "
       pdb=" CA  ASN W   4 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.96e+00
  bond pdb=" C   VAL H  88 "
       pdb=" N   THR H  89 "
    ideal  model  delta    sigma   weight residual
    1.327  1.358 -0.031 2.86e-02 1.22e+03 1.14e+00
  bond pdb=" N   ASN G 268 "
       pdb=" CA  ASN G 268 "
    ideal  model  delta    sigma   weight residual
    1.462  1.452  0.010 9.30e-03 1.16e+04 1.07e+00
  ... (remaining 11413 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.94: 14567
        0.94 -     1.89: 778
        1.89 -     2.83: 84
        2.83 -     3.78: 51
        3.78 -     4.72: 2
  Bond angle restraints: 15482
  Sorted by residual:
  angle pdb=" CA  ILE V  83 "
        pdb=" C   ILE V  83 "
        pdb=" N   ASN V  84 "
      ideal   model   delta    sigma   weight residual
     117.15  120.15   -3.00 7.80e-01 1.64e+00 1.48e+01
  angle pdb=" N   ILE V  83 "
        pdb=" CA  ILE V  83 "
        pdb=" C   ILE V  83 "
      ideal   model   delta    sigma   weight residual
     111.62  113.41   -1.79 7.90e-01 1.60e+00 5.13e+00
  angle pdb=" C   GLY U   7 "
        pdb=" N   SER U   8 "
        pdb=" CA  SER U   8 "
      ideal   model   delta    sigma   weight residual
     120.26  123.01   -2.75 1.34e+00 5.57e-01 4.20e+00
  angle pdb=" N   ASN G 302 "
        pdb=" CA  ASN G 302 "
        pdb=" CB  ASN G 302 "
      ideal   model   delta    sigma   weight residual
     114.27  110.91    3.36 1.64e+00 3.72e-01 4.20e+00
  angle pdb=" N   GLU Q 111 "
        pdb=" CA  GLU Q 111 "
        pdb=" CB  GLU Q 111 "
      ideal   model   delta    sigma   weight residual
     113.65  110.65    3.00 1.47e+00 4.63e-01 4.16e+00
  ... (remaining 15477 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 6739
       17.82 -    35.63: 117
       35.63 -    53.45: 6
       53.45 -    71.27: 3
       71.27 -    89.09: 2
  Dihedral angle restraints: 6867
    sinusoidal: 2746
      harmonic: 4121
  Sorted by residual:
  dihedral pdb=" CA  THR G 235 "
           pdb=" C   THR G 235 "
           pdb=" N   ASN G 236 "
           pdb=" CA  ASN G 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.63  -17.37     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CA  LEU V  68 "
           pdb=" CB  LEU V  68 "
           pdb=" CG  LEU V  68 "
           pdb=" CD1 LEU V  68 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  136.59   43.41     3      1.50e+01 4.44e-03 7.80e+00
  dihedral pdb=" N   LYS U 144 "
           pdb=" CA  LYS U 144 "
           pdb=" CB  LYS U 144 "
           pdb=" CG  LYS U 144 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -99.35   39.35     3      1.50e+01 4.44e-03 6.97e+00
  ... (remaining 6864 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1104
       0.028 -    0.056: 409
       0.056 -    0.084: 52
       0.084 -    0.113: 117
       0.113 -    0.141: 51
  Chirality restraints: 1733
  Sorted by residual:
  chirality pdb=" CA  VAL Q 138 "
            pdb=" N   VAL Q 138 "
            pdb=" C   VAL Q 138 "
            pdb=" CB  VAL Q 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.95e-01
  chirality pdb=" CA  ILE C 170 "
            pdb=" N   ILE C 170 "
            pdb=" C   ILE C 170 "
            pdb=" CB  ILE C 170 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.32e-01
  chirality pdb=" CA  ILE E  27 "
            pdb=" N   ILE E  27 "
            pdb=" C   ILE E  27 "
            pdb=" CB  ILE E  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.28e-01
  ... (remaining 1730 not shown)

  Planarity restraints: 1996
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E  69 "    0.019 5.00e-02 4.00e+02   2.82e-02 1.27e+00
        pdb=" N   PRO E  70 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO E  70 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO E  70 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL Q 138 "   -0.018 5.00e-02 4.00e+02   2.68e-02 1.15e+00
        pdb=" N   PRO Q 139 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO Q 139 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO Q 139 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL E 138 "    0.016 5.00e-02 4.00e+02   2.43e-02 9.44e-01
        pdb=" N   PRO E 139 "   -0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO E 139 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO E 139 "    0.014 5.00e-02 4.00e+02
  ... (remaining 1993 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 96
        2.55 -     3.14: 9081
        3.14 -     3.72: 15788
        3.72 -     4.31: 22837
        4.31 -     4.90: 38850
  Nonbonded interactions: 86652
  Sorted by model distance:
  nonbonded pdb=" OG1 THR G 235 "
            pdb=" O   ARG U  29 "
     model   vdw
     1.959 3.040
  nonbonded pdb=" OG1 THR E   5 "
            pdb=" O   LEU H 148 "
     model   vdw
     2.105 3.040
  nonbonded pdb=" OG1 THR U  99 "
            pdb=" OE2 GLU U 104 "
     model   vdw
     2.124 3.040
  nonbonded pdb=" OH  TYR G 460 "
            pdb=" OG1 THR Q 164 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" O   SER E  30 "
            pdb=" NH1 ARG E 118 "
     model   vdw
     2.172 3.120
  ... (remaining 86647 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'C' and (resid 6 through 67 or resid 80 through 173))
  selection = (chain 'H' and (resid 6 through 37 or resid 47 through 67 or resid 80 through 12 \ 
7 or resid 135 through 173))
  selection = (chain 'Q' and (resid 6 through 37 or resid 47 through 127 or resid 135 through  \ 
173))
}
ncs_group {
  reference = chain 'U'
  selection = chain 'V'
  selection = chain 'W'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.020
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6685
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   0.033  11418  Z= 0.113
  Angle     :  0.487   4.724  15482  Z= 0.303
  Chirality :  0.042   0.141   1733
  Planarity :  0.003   0.028   1996
  Dihedral  :  7.072  89.085   4227
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  1.19 %
    Favored  : 98.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.24), residues: 1379
  helix:  1.39 (0.48), residues: 138
  sheet:  0.87 (0.27), residues: 407
  loop :  0.23 (0.23), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 168 
 TYR   0.005   0.001   TYR W  46 
 PHE   0.005   0.001   PHE E 150 
 TRP   0.004   0.001   TRP H 100 
 HIS   0.003   0.000   HIS G 237 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00188 /  0.11 (11418)
  covalent geometry    : angle       0.48676 /  0.30 (15482)
  hydrogen bonds       : bond        0.28105 / 18.67 (  357)
  hydrogen bonds       : angle       9.42852 /  6.55 (  912)

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

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

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  537 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 534
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   33 TRP cc_start: 0.6505 (m100) cc_final: 0.6022 (m100)
REVERT: C   89 THR cc_start: 0.7842 (p) cc_final: 0.6736 (p)
REVERT: C  110 ASP cc_start: 0.7641 (p0) cc_final: 0.7406 (p0)
REVERT: E   27 ILE cc_start: 0.7936 (mt) cc_final: 0.7394 (mt)
REVERT: E   78 ILE cc_start: 0.6329 (pt) cc_final: 0.6061 (mt)
REVERT: E  114 LEU cc_start: 0.6871 (mt) cc_final: 0.6647 (mp)
REVERT: E  130 SER cc_start: 0.7029 (p) cc_final: 0.6763 (t)
REVERT: E  156 PHE cc_start: 0.7495 (p90) cc_final: 0.6976 (p90)
REVERT: G  316 SER cc_start: 0.7714 (t) cc_final: 0.7465 (m)
REVERT: G  341 GLU cc_start: 0.5743 (mm-30) cc_final: 0.5284 (mm-30)
REVERT: G  356 ASP cc_start: 0.7897 (m-30) cc_final: 0.7248 (m-30)
REVERT: G  359 LEU cc_start: 0.7083 (mt) cc_final: 0.6420 (mp)
REVERT: G  369 ILE cc_start: 0.7252 (pt) cc_final: 0.7036 (mt)
REVERT: G  376 TYR cc_start: 0.7336 (t80) cc_final: 0.6438 (t80)
REVERT: G  427 ASP cc_start: 0.7165 (m-30) cc_final: 0.6902 (t70)
REVERT: G  459 ASN cc_start: 0.7529 (t0) cc_final: 0.7086 (p0)
REVERT: H   12 LEU cc_start: 0.8059 (mt) cc_final: 0.7494 (mt)
REVERT: H   16 LEU cc_start: 0.7746 (tp) cc_final: 0.7449 (tp)
REVERT: H   41 GLN cc_start: 0.8069 (mp10) cc_final: 0.7788 (mp10)
REVERT: H   61 VAL cc_start: 0.8560 (t) cc_final: 0.8346 (m)
REVERT: H   68 LYS cc_start: 0.8294 (mttt) cc_final: 0.8055 (mmtm)
REVERT: H  102 TYR cc_start: 0.6661 (t80) cc_final: 0.6055 (t80)
REVERT: H  105 SER cc_start: 0.8075 (t) cc_final: 0.7595 (t)
REVERT: H  143 GLU cc_start: 0.8269 (tp30) cc_final: 0.7975 (tm-30)
REVERT: H  154 LYS cc_start: 0.8091 (mttp) cc_final: 0.7761 (mtmt)
REVERT: Q   87 GLU cc_start: 0.4010 (mt-10) cc_final: 0.3728 (tm-30)
REVERT: Q  105 SER cc_start: 0.7516 (t) cc_final: 0.7059 (t)
REVERT: U    8 SER cc_start: 0.8834 (p) cc_final: 0.8549 (p)
REVERT: U   48 LYS cc_start: 0.7414 (tttt) cc_final: 0.7144 (ttpt)
REVERT: U   89 TYR cc_start: 0.7042 (t80) cc_final: 0.6477 (t80)
REVERT: U   92 ASN cc_start: 0.5343 (t0) cc_final: 0.5010 (t0)
REVERT: U   97 LYS cc_start: 0.7557 (ptpt) cc_final: 0.7057 (pttt)
REVERT: U  119 GLU cc_start: 0.7034 (tt0) cc_final: 0.6766 (tm-30)
REVERT: U  126 GLN cc_start: 0.6835 (mt0) cc_final: 0.6575 (mm-40)
REVERT: U  151 ASP cc_start: 0.8428 (t0) cc_final: 0.8207 (t0)
REVERT: V   10 TYR cc_start: 0.5850 (m-80) cc_final: 0.5373 (m-80)
REVERT: V   39 MET cc_start: 0.8201 (ttt) cc_final: 0.7053 (ttt)
REVERT: V  159 THR cc_start: 0.8300 (p) cc_final: 0.8030 (p)
REVERT: V  165 LEU cc_start: 0.8094 (tp) cc_final: 0.7892 (tp)
REVERT: W   15 ASP cc_start: 0.6241 (t0) cc_final: 0.6033 (t0)
REVERT: W   38 GLU cc_start: 0.7023 (tt0) cc_final: 0.6785 (mt-10)
REVERT: W   68 LEU cc_start: 0.8083 (tp) cc_final: 0.7729 (pp)
REVERT: W   89 TYR cc_start: 0.6959 (t80) cc_final: 0.6673 (t80)
REVERT: W  105 THR cc_start: 0.7770 (p) cc_final: 0.7546 (t)
REVERT: W  151 ASP cc_start: 0.7615 (t0) cc_final: 0.7321 (t0)
REVERT: W  161 MET cc_start: 0.6601 (tpt) cc_final: 0.5616 (tpp)
REVERT: W  162 ASP cc_start: 0.4721 (m-30) cc_final: 0.3646 (m-30)
REVERT: W  166 TYR cc_start: 0.7079 (t80) cc_final: 0.6701 (t80)
  outliers start: 3
  outliers final: 2
  residues processed: 535
  average time/residue: 0.0942
  time to fit residues: 72.9400
Evaluate side-chains
  336 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 334
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C   9 HIS
E 136 ASN
** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 258 ASN
G 320 ASN
Q 157 GLN
U  26 ASN
V 168 GLN
W 126 GLN
W 150 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.146972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.128691 restraints weight = 24708.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.131702 restraints weight = 15374.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.133742 restraints weight = 10524.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.135190 restraints weight = 7833.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.136243 restraints weight = 6231.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6965
moved from start:          0.3113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11418  Z= 0.173
  Angle     :  0.656   7.908  15482  Z= 0.347
  Chirality :  0.048   0.171   1733
  Planarity :  0.005   0.044   1996
  Dihedral  :  4.096  20.581   1527
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  2.77 %
    Favored  : 96.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.23), residues: 1379
  helix:  0.01 (0.39), residues: 166
  sheet:  0.79 (0.26), residues: 383
  loop : -0.14 (0.22), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C  65 
 TYR   0.024   0.002   TYR G 256 
 PHE   0.027   0.002   PHE C 156 
 TRP   0.025   0.002   TRP H 100 
 HIS   0.005   0.002   HIS Q   9 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00374 /  0.17 (11418)
  covalent geometry    : angle       0.65636 /  0.35 (15482)
  hydrogen bonds       : bond        0.05944 /  3.92 (  357)
  hydrogen bonds       : angle       7.26323 /  5.01 (  912)

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

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

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  390 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 386
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   33 TRP cc_start: 0.6832 (m100) cc_final: 0.6266 (m100)
REVERT: C  102 TYR cc_start: 0.6825 (t80) cc_final: 0.6024 (t80)
REVERT: C  104 GLU cc_start: 0.5614 (tp30) cc_final: 0.5072 (tp30)
REVERT: C  106 SER cc_start: 0.7759 (m) cc_final: 0.7539 (p)
REVERT: E   12 LEU cc_start: 0.8120 (tp) cc_final: 0.7820 (tp)
REVERT: E   78 ILE cc_start: 0.6568 (pt) cc_final: 0.6096 (mt)
REVERT: E  118 ARG cc_start: 0.6678 (mtt90) cc_final: 0.6301 (mtt90)
REVERT: E  130 SER cc_start: 0.7173 (p) cc_final: 0.6965 (t)
REVERT: G  199 THR cc_start: 0.8314 (p) cc_final: 0.7997 (t)
REVERT: G  213 PHE cc_start: 0.8564 (t80) cc_final: 0.8342 (t80)
REVERT: G  268 ASN cc_start: 0.8393 (m-40) cc_final: 0.7514 (m-40)
REVERT: G  309 MET cc_start: 0.8293 (mtt) cc_final: 0.8045 (mtt)
REVERT: G  341 GLU cc_start: 0.5715 (mm-30) cc_final: 0.5494 (mm-30)
REVERT: G  369 ILE cc_start: 0.7672 (pt) cc_final: 0.7408 (mt)
REVERT: G  376 TYR cc_start: 0.7081 (t80) cc_final: 0.5940 (t80)
REVERT: H   12 LEU cc_start: 0.8258 (mt) cc_final: 0.7852 (mt)
REVERT: H   96 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7675 (mm-30)
REVERT: H  105 SER cc_start: 0.8161 (t) cc_final: 0.7896 (t)
REVERT: H  119 GLN cc_start: 0.7231 (mt0) cc_final: 0.6931 (mt0)
REVERT: H  132 ILE cc_start: 0.6496 (mt) cc_final: 0.6011 (mt)
REVERT: H  151 PHE cc_start: 0.7857 (t80) cc_final: 0.7344 (t80)
REVERT: H  156 PHE cc_start: 0.7709 (p90) cc_final: 0.7461 (p90)
REVERT: U   40 GLN cc_start: 0.8352 (tt0) cc_final: 0.8104 (tt0)
REVERT: U   48 LYS cc_start: 0.7594 (tttt) cc_final: 0.7056 (ttpt)
REVERT: U   89 TYR cc_start: 0.6815 (t80) cc_final: 0.6532 (t80)
REVERT: U   97 LYS cc_start: 0.7377 (ptpt) cc_final: 0.6861 (pttt)
REVERT: U  119 GLU cc_start: 0.7114 (tt0) cc_final: 0.6852 (tm-30)
REVERT: U  126 GLN cc_start: 0.6885 (mt0) cc_final: 0.6660 (mm-40)
REVERT: U  168 GLN cc_start: 0.6295 (pm20) cc_final: 0.5652 (pm20)
REVERT: V   10 TYR cc_start: 0.6180 (m-80) cc_final: 0.5591 (m-80)
REVERT: V   24 LEU cc_start: 0.7148 (mm) cc_final: 0.6511 (mt)
REVERT: V   38 GLU cc_start: 0.7735 (tt0) cc_final: 0.7284 (tt0)
REVERT: V   39 MET cc_start: 0.8607 (ttt) cc_final: 0.8137 (ttt)
REVERT: V   49 ASN cc_start: 0.8150 (t0) cc_final: 0.7766 (t0)
REVERT: V  165 LEU cc_start: 0.8205 (tp) cc_final: 0.7467 (tp)
REVERT: W   24 LEU cc_start: 0.8460 (mt) cc_final: 0.8066 (mt)
REVERT: W   28 ASP cc_start: 0.7906 (t0) cc_final: 0.7278 (t0)
REVERT: W   68 LEU cc_start: 0.8205 (tp) cc_final: 0.7793 (pt)
REVERT: W   83 ILE cc_start: 0.7733 (mt) cc_final: 0.7395 (mt)
REVERT: W   87 ILE cc_start: 0.9218 (mt) cc_final: 0.8971 (mt)
REVERT: W   89 TYR cc_start: 0.7440 (t80) cc_final: 0.7039 (t80)
REVERT: W   99 THR cc_start: 0.7076 (p) cc_final: 0.6755 (t)
REVERT: W  150 ASN cc_start: 0.7627 (OUTLIER) cc_final: 0.7352 (t0)
REVERT: W  151 ASP cc_start: 0.7715 (t0) cc_final: 0.7310 (t0)
  outliers start: 4
  outliers final: 0
  residues processed: 389
  average time/residue: 0.0929
  time to fit residues: 52.7865
Evaluate side-chains
  303 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 302
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 63 optimal weight:    0.0470
   chunk 60 optimal weight:    0.0670
   chunk 0 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   chunk 112 optimal weight:    3.9990
   chunk 95 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   chunk 89 optimal weight:    3.9990
   overall best weight:    1.2222

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 158 ASN
** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 220 ASN
** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 258 ASN
G 310 GLN
H 157 GLN
** V  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.145194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.126705 restraints weight = 24827.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.129788 restraints weight = 15417.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.131910 restraints weight = 10541.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.133388 restraints weight = 7813.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.134352 restraints weight = 6195.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
moved from start:          0.3797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11418  Z= 0.162
  Angle     :  0.608   7.071  15482  Z= 0.323
  Chirality :  0.046   0.164   1733
  Planarity :  0.005   0.056   1996
  Dihedral  :  4.418  19.406   1527
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.22), residues: 1379
  helix:  0.02 (0.39), residues: 167
  sheet:  0.47 (0.26), residues: 375
  loop : -0.33 (0.22), residues: 837

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG C  65 
 TYR   0.029   0.002   TYR G 256 
 PHE   0.017   0.002   PHE H 156 
 TRP   0.025   0.002   TRP C  85 
 HIS   0.006   0.002   HIS G 216 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.16 (11418)
  covalent geometry    : angle       0.60758 /  0.32 (15482)
  hydrogen bonds       : bond        0.05441 /  3.57 (  357)
  hydrogen bonds       : angle       6.81135 /  4.69 (  912)

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

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

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  345 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 345
  time to evaluate  : 0.447 
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: C   33 TRP cc_start: 0.6950 (m100) cc_final: 0.6525 (m100)
REVERT: C  106 SER cc_start: 0.7779 (m) cc_final: 0.7557 (p)
REVERT: C  136 ASN cc_start: 0.8701 (p0) cc_final: 0.7949 (p0)
REVERT: E   27 ILE cc_start: 0.8082 (mm) cc_final: 0.7687 (mm)
REVERT: E   78 ILE cc_start: 0.6371 (pt) cc_final: 0.5932 (mt)
REVERT: E  118 ARG cc_start: 0.6615 (mtt90) cc_final: 0.6368 (mtt90)
REVERT: E  130 SER cc_start: 0.7014 (p) cc_final: 0.6750 (t)
REVERT: G  213 PHE cc_start: 0.8632 (t80) cc_final: 0.8252 (t80)
REVERT: G  258 ASN cc_start: 0.8513 (m-40) cc_final: 0.8232 (m-40)
REVERT: G  268 ASN cc_start: 0.8454 (m-40) cc_final: 0.7563 (m-40)
REVERT: G  309 MET cc_start: 0.8275 (mtt) cc_final: 0.8006 (mtt)
REVERT: G  316 SER cc_start: 0.7889 (t) cc_final: 0.7683 (t)
REVERT: G  341 GLU cc_start: 0.5964 (mm-30) cc_final: 0.5657 (mm-30)
REVERT: G  369 ILE cc_start: 0.7674 (pt) cc_final: 0.7429 (mt)
REVERT: G  374 GLN cc_start: 0.7521 (tp-100) cc_final: 0.6763 (mm-40)
REVERT: G  376 TYR cc_start: 0.7066 (t80) cc_final: 0.6106 (t80)
REVERT: G  461 LEU cc_start: 0.8325 (tp) cc_final: 0.7987 (tp)
REVERT: H   25 LEU cc_start: 0.8381 (tp) cc_final: 0.8143 (tp)
REVERT: H   51 GLU cc_start: 0.8112 (pt0) cc_final: 0.7886 (pt0)
REVERT: H   76 ASN cc_start: 0.6788 (m-40) cc_final: 0.5949 (p0)
REVERT: H  118 ARG cc_start: 0.6211 (mtt-85) cc_final: 0.5501 (mtm-85)
REVERT: U   40 GLN cc_start: 0.8406 (tt0) cc_final: 0.8150 (tt0)
REVERT: U   48 LYS cc_start: 0.7452 (tttt) cc_final: 0.7009 (tmmt)
REVERT: U   89 TYR cc_start: 0.7197 (t80) cc_final: 0.6343 (t80)
REVERT: U   97 LYS cc_start: 0.7491 (ptpt) cc_final: 0.6933 (pttt)
REVERT: U  119 GLU cc_start: 0.7132 (tt0) cc_final: 0.6840 (tm-30)
REVERT: U  125 ASP cc_start: 0.7572 (t0) cc_final: 0.6756 (t0)
REVERT: U  126 GLN cc_start: 0.6819 (mt0) cc_final: 0.6295 (mm-40)
REVERT: U  168 GLN cc_start: 0.6084 (pm20) cc_final: 0.5327 (pm20)
REVERT: V   10 TYR cc_start: 0.6174 (m-80) cc_final: 0.5636 (m-80)
REVERT: V   24 LEU cc_start: 0.7283 (mm) cc_final: 0.6555 (mt)
REVERT: V   38 GLU cc_start: 0.7612 (tt0) cc_final: 0.7343 (tt0)
REVERT: V   39 MET cc_start: 0.8751 (ttt) cc_final: 0.8358 (ttt)
REVERT: V   49 ASN cc_start: 0.8200 (t0) cc_final: 0.7837 (t0)
REVERT: V   87 ILE cc_start: 0.9231 (mt) cc_final: 0.9028 (mp)
REVERT: V  165 LEU cc_start: 0.7901 (tp) cc_final: 0.7622 (tp)
REVERT: W   19 ASP cc_start: 0.7749 (m-30) cc_final: 0.7495 (m-30)
REVERT: W   28 ASP cc_start: 0.7824 (t0) cc_final: 0.7311 (t0)
REVERT: W   56 LYS cc_start: 0.6596 (ttpp) cc_final: 0.5485 (ptpp)
REVERT: W   59 ASP cc_start: 0.7536 (m-30) cc_final: 0.6845 (m-30)
REVERT: W   68 LEU cc_start: 0.8261 (tp) cc_final: 0.7785 (pt)
REVERT: W   87 ILE cc_start: 0.9302 (mt) cc_final: 0.9087 (mt)
REVERT: W   89 TYR cc_start: 0.7385 (t80) cc_final: 0.6979 (t80)
REVERT: W  151 ASP cc_start: 0.7829 (t0) cc_final: 0.7475 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 345
  average time/residue: 0.0858
  time to fit residues: 43.1336
Evaluate side-chains
  280 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 280
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 67 optimal weight:    5.9990
   chunk 117 optimal weight:    7.9990
   chunk 122 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 83 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 0 optimal weight:    7.9990
   chunk 50 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    3.7588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 158 ASN
** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 162 GLN
U  26 ASN
** V  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 126 GLN
** W  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
W 150 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.131509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.113371 restraints weight = 25314.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.116100 restraints weight = 16013.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.117982 restraints weight = 11174.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.119250 restraints weight = 8421.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.120207 restraints weight = 6796.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.5022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.094  11418  Z= 0.377
  Angle     :  0.920   8.097  15482  Z= 0.496
  Chirality :  0.055   0.194   1733
  Planarity :  0.007   0.072   1996
  Dihedral  :  6.423  25.878   1527
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 17.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  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: -1.27 (0.21), residues: 1379
  helix: -0.94 (0.37), residues: 169
  sheet: -0.14 (0.26), residues: 355
  loop : -1.15 (0.20), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C  65 
 TYR   0.034   0.003   TYR G 256 
 PHE   0.043   0.004   PHE G 233 
 TRP   0.025   0.003   TRP C  85 
 HIS   0.009   0.003   HIS G 237 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00866 /  0.38 (11418)
  covalent geometry    : angle       0.91987 /  0.50 (15482)
  hydrogen bonds       : bond        0.06802 /  4.44 (  357)
  hydrogen bonds       : angle       7.42603 /  5.13 (  912)

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

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

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 297
  time to evaluate  : 0.367 
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: C   29 LYS cc_start: 0.7925 (tptp) cc_final: 0.7433 (tppt)
REVERT: C   83 LYS cc_start: 0.7110 (ptpt) cc_final: 0.6480 (ptmm)
REVERT: E   49 LEU cc_start: 0.7133 (mt) cc_final: 0.6884 (mt)
REVERT: E   65 ARG cc_start: 0.8399 (ptt180) cc_final: 0.8173 (ptt180)
REVERT: E   78 ILE cc_start: 0.6442 (pt) cc_final: 0.5925 (mt)
REVERT: E  130 SER cc_start: 0.7095 (p) cc_final: 0.6598 (t)
REVERT: E  149 LEU cc_start: 0.8065 (tp) cc_final: 0.7545 (tp)
REVERT: E  150 PHE cc_start: 0.8240 (m-80) cc_final: 0.7905 (m-10)
REVERT: G  341 GLU cc_start: 0.6362 (mm-30) cc_final: 0.6103 (mm-30)
REVERT: G  369 ILE cc_start: 0.7958 (pt) cc_final: 0.7604 (mt)
REVERT: G  376 TYR cc_start: 0.7315 (t80) cc_final: 0.7014 (t80)
REVERT: H  152 ASP cc_start: 0.8532 (t70) cc_final: 0.8253 (t0)
REVERT: U   24 LEU cc_start: 0.7873 (mt) cc_final: 0.7486 (mt)
REVERT: U   89 TYR cc_start: 0.6905 (t80) cc_final: 0.6279 (t80)
REVERT: U   91 ASP cc_start: 0.7564 (p0) cc_final: 0.7186 (p0)
REVERT: U   97 LYS cc_start: 0.7655 (ptpt) cc_final: 0.7200 (pttt)
REVERT: U  125 ASP cc_start: 0.8202 (t0) cc_final: 0.7476 (t0)
REVERT: U  126 GLN cc_start: 0.6894 (mt0) cc_final: 0.6349 (mm-40)
REVERT: U  143 GLU cc_start: 0.6640 (mt-10) cc_final: 0.6429 (mt-10)
REVERT: U  168 GLN cc_start: 0.5464 (pm20) cc_final: 0.4858 (pm20)
REVERT: V   10 TYR cc_start: 0.6356 (m-80) cc_final: 0.5669 (m-80)
REVERT: V   39 MET cc_start: 0.8747 (ttt) cc_final: 0.8351 (ttt)
REVERT: V   49 ASN cc_start: 0.8274 (t0) cc_final: 0.7823 (t0)
REVERT: V  103 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7848 (tttp)
REVERT: V  123 LEU cc_start: 0.7915 (mt) cc_final: 0.7663 (mt)
REVERT: V  141 LEU cc_start: 0.6000 (tp) cc_final: 0.5590 (tp)
REVERT: V  165 LEU cc_start: 0.8073 (tp) cc_final: 0.7525 (tp)
REVERT: W   28 ASP cc_start: 0.8259 (t0) cc_final: 0.7797 (t0)
REVERT: W   56 LYS cc_start: 0.6366 (ttpp) cc_final: 0.5524 (ptpp)
REVERT: W   59 ASP cc_start: 0.7592 (m-30) cc_final: 0.7182 (m-30)
REVERT: W   68 LEU cc_start: 0.8053 (tp) cc_final: 0.7635 (pt)
REVERT: W   89 TYR cc_start: 0.8039 (t80) cc_final: 0.7567 (t80)
REVERT: W  151 ASP cc_start: 0.8200 (t0) cc_final: 0.7847 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 297
  average time/residue: 0.0860
  time to fit residues: 37.6311
Evaluate side-chains
  245 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 78 optimal weight:    9.9990
   chunk 44 optimal weight:    0.7980
   chunk 114 optimal weight:    3.9990
   chunk 72 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9980
   chunk 119 optimal weight:    0.1980
   chunk 14 optimal weight:    0.8980
   chunk 109 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 110 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.141062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.123107 restraints weight = 24547.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.125823 restraints weight = 15461.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.127640 restraints weight = 10777.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.128989 restraints weight = 8173.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.129828 restraints weight = 6597.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.5006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  11418  Z= 0.143
  Angle     :  0.645   6.828  15482  Z= 0.342
  Chirality :  0.047   0.177   1733
  Planarity :  0.005   0.049   1996
  Dihedral  :  5.317  20.173   1527
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.22), residues: 1379
  helix: -0.32 (0.39), residues: 156
  sheet: -0.24 (0.26), residues: 381
  loop : -0.75 (0.21), residues: 842

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  65 
 TYR   0.026   0.002   TYR Q 117 
 PHE   0.016   0.002   PHE H 169 
 TRP   0.016   0.001   TRP H 100 
 HIS   0.002   0.001   HIS G 216 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.14 (11418)
  covalent geometry    : angle       0.64511 /  0.34 (15482)
  hydrogen bonds       : bond        0.04926 /  3.17 (  357)
  hydrogen bonds       : angle       6.64540 /  4.54 (  912)

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

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

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 337
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   78 ILE cc_start: 0.6223 (pt) cc_final: 0.5869 (mt)
REVERT: E  118 ARG cc_start: 0.7056 (mtt90) cc_final: 0.6548 (mtt180)
REVERT: E  130 SER cc_start: 0.7028 (p) cc_final: 0.6592 (t)
REVERT: E  149 LEU cc_start: 0.8274 (tp) cc_final: 0.7894 (tp)
REVERT: E  150 PHE cc_start: 0.8141 (m-80) cc_final: 0.7761 (m-80)
REVERT: G  268 ASN cc_start: 0.8350 (m110) cc_final: 0.7526 (m-40)
REVERT: G  296 TYR cc_start: 0.7766 (m-80) cc_final: 0.7458 (m-80)
REVERT: G  369 ILE cc_start: 0.7741 (pt) cc_final: 0.7462 (mt)
REVERT: G  376 TYR cc_start: 0.7126 (t80) cc_final: 0.6017 (t80)
REVERT: G  441 TYR cc_start: 0.7645 (t80) cc_final: 0.7433 (t80)
REVERT: H   26 THR cc_start: 0.5992 (t) cc_final: 0.5646 (t)
REVERT: H   55 TYR cc_start: 0.7563 (m-10) cc_final: 0.5915 (m-10)
REVERT: U   48 LYS cc_start: 0.7698 (tttt) cc_final: 0.7039 (ttpt)
REVERT: U   89 TYR cc_start: 0.6798 (t80) cc_final: 0.6319 (t80)
REVERT: U   97 LYS cc_start: 0.7612 (ptpt) cc_final: 0.6989 (pttt)
REVERT: U  125 ASP cc_start: 0.8221 (t0) cc_final: 0.7531 (t0)
REVERT: U  126 GLN cc_start: 0.6898 (mt0) cc_final: 0.6332 (mm-40)
REVERT: U  127 THR cc_start: 0.8063 (m) cc_final: 0.7543 (p)
REVERT: U  145 MET cc_start: 0.7471 (mtp) cc_final: 0.7212 (mtp)
REVERT: U  158 TYR cc_start: 0.7875 (m-80) cc_final: 0.7671 (m-80)
REVERT: U  167 ILE cc_start: 0.8335 (mt) cc_final: 0.8107 (tp)
REVERT: V   10 TYR cc_start: 0.6336 (m-80) cc_final: 0.5971 (m-80)
REVERT: V   49 ASN cc_start: 0.8257 (t0) cc_final: 0.7600 (t0)
REVERT: V  114 ILE cc_start: 0.9070 (tp) cc_final: 0.8825 (tt)
REVERT: W   11 LEU cc_start: 0.8269 (mt) cc_final: 0.7875 (mt)
REVERT: W   56 LYS cc_start: 0.6219 (ttpp) cc_final: 0.5360 (ptpp)
REVERT: W   59 ASP cc_start: 0.7191 (m-30) cc_final: 0.6620 (m-30)
REVERT: W   68 LEU cc_start: 0.8168 (tp) cc_final: 0.7664 (pt)
REVERT: W   87 ILE cc_start: 0.9341 (mt) cc_final: 0.9038 (mt)
REVERT: W   89 TYR cc_start: 0.7747 (t80) cc_final: 0.7397 (t80)
REVERT: W  151 ASP cc_start: 0.7954 (t0) cc_final: 0.7604 (t0)
REVERT: W  161 MET cc_start: 0.5102 (tpp) cc_final: 0.4437 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 337
  average time/residue: 0.0935
  time to fit residues: 46.3174
Evaluate side-chains
  275 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 275
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 101 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 61 optimal weight:    8.9990
   chunk 2 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  38 ASN
U  72 ASN
W 150 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.139599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.121139 restraints weight = 25118.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.124028 restraints weight = 15523.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.125989 restraints weight = 10664.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.127254 restraints weight = 7965.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.128278 restraints weight = 6456.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7147
moved from start:          0.5201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11418  Z= 0.173
  Angle     :  0.658   9.092  15482  Z= 0.349
  Chirality :  0.047   0.192   1733
  Planarity :  0.005   0.050   1996
  Dihedral  :  5.270  19.606   1527
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.81 (0.22), residues: 1379
  helix: -0.44 (0.38), residues: 169
  sheet: -0.08 (0.25), residues: 383
  loop : -0.74 (0.21), residues: 827

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  65 
 TYR   0.022   0.002   TYR E 117 
 PHE   0.019   0.002   PHE Q 169 
 TRP   0.029   0.002   TRP C  85 
 HIS   0.004   0.002   HIS G 216 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00396 /  0.17 (11418)
  covalent geometry    : angle       0.65792 /  0.35 (15482)
  hydrogen bonds       : bond        0.04925 /  3.14 (  357)
  hydrogen bonds       : angle       6.58550 /  4.48 (  912)

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

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

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 318
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   29 LYS cc_start: 0.6862 (tppt) cc_final: 0.6483 (tptt)
REVERT: C   80 TYR cc_start: 0.7079 (p90) cc_final: 0.6834 (p90)
REVERT: C  102 TYR cc_start: 0.6688 (t80) cc_final: 0.6345 (t80)
REVERT: C  111 GLU cc_start: 0.7884 (tp30) cc_final: 0.7518 (tp30)
REVERT: C  136 ASN cc_start: 0.8471 (p0) cc_final: 0.7890 (p0)
REVERT: E   78 ILE cc_start: 0.5947 (pt) cc_final: 0.5678 (mt)
REVERT: E  108 VAL cc_start: 0.8253 (p) cc_final: 0.8044 (p)
REVERT: E  118 ARG cc_start: 0.6973 (mtt90) cc_final: 0.6147 (mtt180)
REVERT: E  119 GLN cc_start: 0.7351 (tt0) cc_final: 0.6936 (tt0)
REVERT: E  130 SER cc_start: 0.6897 (p) cc_final: 0.6494 (t)
REVERT: E  149 LEU cc_start: 0.8259 (tp) cc_final: 0.7925 (tp)
REVERT: E  150 PHE cc_start: 0.8332 (m-80) cc_final: 0.7999 (m-80)
REVERT: E  171 VAL cc_start: 0.6420 (p) cc_final: 0.6110 (p)
REVERT: G  296 TYR cc_start: 0.7741 (m-80) cc_final: 0.7413 (m-80)
REVERT: G  369 ILE cc_start: 0.7854 (pt) cc_final: 0.7536 (mt)
REVERT: H   55 TYR cc_start: 0.7710 (m-10) cc_final: 0.6235 (m-10)
REVERT: U   48 LYS cc_start: 0.7574 (tttt) cc_final: 0.7068 (ttpt)
REVERT: U   87 ILE cc_start: 0.9110 (mp) cc_final: 0.8889 (mp)
REVERT: U   89 TYR cc_start: 0.6818 (t80) cc_final: 0.6257 (t80)
REVERT: U   97 LYS cc_start: 0.7585 (ptpt) cc_final: 0.7027 (pttt)
REVERT: U  125 ASP cc_start: 0.8269 (t0) cc_final: 0.7470 (t0)
REVERT: U  126 GLN cc_start: 0.6911 (mt0) cc_final: 0.6271 (mm-40)
REVERT: U  127 THR cc_start: 0.8102 (m) cc_final: 0.7532 (p)
REVERT: V   10 TYR cc_start: 0.6342 (m-80) cc_final: 0.5868 (m-80)
REVERT: V   49 ASN cc_start: 0.8281 (t0) cc_final: 0.7833 (t0)
REVERT: V   86 LYS cc_start: 0.7683 (mtmm) cc_final: 0.7419 (mtpp)
REVERT: V  114 ILE cc_start: 0.9083 (tp) cc_final: 0.8859 (tt)
REVERT: V  162 ASP cc_start: 0.6700 (m-30) cc_final: 0.6495 (m-30)
REVERT: W    6 LYS cc_start: 0.7735 (mmpt) cc_final: 0.7448 (mptt)
REVERT: W   11 LEU cc_start: 0.8259 (mt) cc_final: 0.7857 (mt)
REVERT: W   38 GLU cc_start: 0.6420 (mm-30) cc_final: 0.5938 (tt0)
REVERT: W   56 LYS cc_start: 0.6324 (ttpp) cc_final: 0.5390 (ptpp)
REVERT: W   59 ASP cc_start: 0.7315 (m-30) cc_final: 0.6960 (m-30)
REVERT: W   68 LEU cc_start: 0.8195 (tp) cc_final: 0.7654 (pt)
REVERT: W   87 ILE cc_start: 0.9330 (mt) cc_final: 0.9091 (mt)
REVERT: W   89 TYR cc_start: 0.7713 (t80) cc_final: 0.7345 (t80)
REVERT: W  151 ASP cc_start: 0.7956 (t0) cc_final: 0.7637 (t0)
REVERT: W  161 MET cc_start: 0.5132 (tpp) cc_final: 0.4469 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 318
  average time/residue: 0.0960
  time to fit residues: 44.8809
Evaluate side-chains
  275 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 275
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 100 optimal weight:    5.9990
   chunk 87 optimal weight:    6.9990
   chunk 95 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 117 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   chunk 105 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 73 optimal weight:    0.1980
   chunk 41 optimal weight:    0.8980
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 201 GLN
** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  26 ASN
** U  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  72 ASN
** V  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.140899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.122627 restraints weight = 24249.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.125500 restraints weight = 14961.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.127483 restraints weight = 10257.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.128880 restraints weight = 7635.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.129868 restraints weight = 6065.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.5270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11418  Z= 0.134
  Angle     :  0.625   9.284  15482  Z= 0.329
  Chirality :  0.047   0.206   1733
  Planarity :  0.005   0.050   1996
  Dihedral  :  5.037  19.853   1527
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.22), residues: 1379
  helix: -0.31 (0.40), residues: 157
  sheet: -0.06 (0.25), residues: 389
  loop : -0.57 (0.22), residues: 833

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG C 168 
 TYR   0.022   0.002   TYR E 117 
 PHE   0.017   0.002   PHE Q 169 
 TRP   0.018   0.002   TRP C  85 
 HIS   0.002   0.001   HIS G 216 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.13 (11418)
  covalent geometry    : angle       0.62548 /  0.33 (15482)
  hydrogen bonds       : bond        0.04561 /  2.95 (  357)
  hydrogen bonds       : angle       6.47107 /  4.40 (  912)

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

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

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 319
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   25 LEU cc_start: 0.7027 (tp) cc_final: 0.6787 (tt)
REVERT: C  111 GLU cc_start: 0.7874 (tp30) cc_final: 0.7670 (tp30)
REVERT: E  108 VAL cc_start: 0.8091 (p) cc_final: 0.7854 (p)
REVERT: E  119 GLN cc_start: 0.7218 (tt0) cc_final: 0.6930 (tt0)
REVERT: E  130 SER cc_start: 0.7176 (p) cc_final: 0.6786 (t)
REVERT: E  149 LEU cc_start: 0.8321 (tp) cc_final: 0.7975 (tp)
REVERT: E  150 PHE cc_start: 0.8327 (m-80) cc_final: 0.7994 (m-80)
REVERT: E  171 VAL cc_start: 0.6537 (p) cc_final: 0.6117 (p)
REVERT: G  213 PHE cc_start: 0.8483 (t80) cc_final: 0.8268 (t80)
REVERT: G  268 ASN cc_start: 0.8433 (m110) cc_final: 0.7501 (m-40)
REVERT: G  296 TYR cc_start: 0.7791 (m-80) cc_final: 0.7271 (m-80)
REVERT: G  369 ILE cc_start: 0.7848 (pt) cc_final: 0.7557 (mt)
REVERT: G  376 TYR cc_start: 0.7169 (t80) cc_final: 0.6028 (t80)
REVERT: G  393 PHE cc_start: 0.7150 (t80) cc_final: 0.6918 (t80)
REVERT: G  411 SER cc_start: 0.7328 (t) cc_final: 0.7038 (t)
REVERT: H   26 THR cc_start: 0.5919 (t) cc_final: 0.5595 (t)
REVERT: H   51 GLU cc_start: 0.8447 (pm20) cc_final: 0.7989 (pt0)
REVERT: H   55 TYR cc_start: 0.7716 (m-10) cc_final: 0.6077 (m-10)
REVERT: H  152 ASP cc_start: 0.8388 (t70) cc_final: 0.8133 (t0)
REVERT: U   48 LYS cc_start: 0.7303 (tttt) cc_final: 0.6881 (tmmt)
REVERT: U   89 TYR cc_start: 0.6820 (t80) cc_final: 0.6128 (t80)
REVERT: U   97 LYS cc_start: 0.7394 (ptpt) cc_final: 0.6954 (pttt)
REVERT: U  125 ASP cc_start: 0.8209 (t0) cc_final: 0.7435 (t0)
REVERT: U  126 GLN cc_start: 0.6872 (mt0) cc_final: 0.6262 (mm-40)
REVERT: U  127 THR cc_start: 0.8033 (m) cc_final: 0.7465 (p)
REVERT: V   10 TYR cc_start: 0.6303 (m-80) cc_final: 0.5865 (m-80)
REVERT: V   13 ARG cc_start: 0.6859 (mtt180) cc_final: 0.6577 (mtt180)
REVERT: V   24 LEU cc_start: 0.7325 (mm) cc_final: 0.6731 (mt)
REVERT: V   49 ASN cc_start: 0.8153 (t0) cc_final: 0.7732 (t0)
REVERT: V   86 LYS cc_start: 0.7596 (mtmm) cc_final: 0.7392 (mtpp)
REVERT: W    6 LYS cc_start: 0.7644 (mmpt) cc_final: 0.7414 (mptt)
REVERT: W   11 LEU cc_start: 0.8201 (mt) cc_final: 0.7834 (mt)
REVERT: W   56 LYS cc_start: 0.6228 (ttpp) cc_final: 0.5421 (ptpp)
REVERT: W   59 ASP cc_start: 0.7271 (m-30) cc_final: 0.6897 (m-30)
REVERT: W   68 LEU cc_start: 0.8207 (tp) cc_final: 0.7661 (pt)
REVERT: W   87 ILE cc_start: 0.9315 (mt) cc_final: 0.9085 (mt)
REVERT: W   89 TYR cc_start: 0.7626 (t80) cc_final: 0.7259 (t80)
REVERT: W  151 ASP cc_start: 0.7956 (t0) cc_final: 0.7612 (t0)
REVERT: W  161 MET cc_start: 0.5321 (tpp) cc_final: 0.4697 (tpp)
REVERT: W  162 ASP cc_start: 0.4279 (m-30) cc_final: 0.4070 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 319
  average time/residue: 0.0920
  time to fit residues: 42.7508
Evaluate side-chains
  265 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 265
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 121 optimal weight:    1.9990
   chunk 116 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 113 optimal weight:    5.9990
   chunk 79 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    1.7588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 374 GLN
U  26 ASN
** U  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  72 ASN
W  72 ASN
W 150 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.138516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.120580 restraints weight = 24891.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.123273 restraints weight = 15601.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.125139 restraints weight = 10850.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.126421 restraints weight = 8188.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.127219 restraints weight = 6617.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7173
moved from start:          0.5460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  11418  Z= 0.194
  Angle     :  0.675   8.733  15482  Z= 0.358
  Chirality :  0.048   0.205   1733
  Planarity :  0.005   0.052   1996
  Dihedral  :  5.301  19.144   1527
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.22), residues: 1379
  helix: -0.41 (0.39), residues: 169
  sheet: -0.05 (0.26), residues: 385
  loop : -0.71 (0.21), residues: 825

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 168 
 TYR   0.027   0.002   TYR E  80 
 PHE   0.021   0.002   PHE G 233 
 TRP   0.011   0.002   TRP E 100 
 HIS   0.004   0.002   HIS G 216 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00452 /  0.19 (11418)
  covalent geometry    : angle       0.67467 /  0.36 (15482)
  hydrogen bonds       : bond        0.04911 /  3.20 (  357)
  hydrogen bonds       : angle       6.49584 /  4.44 (  912)

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

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

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 312
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   25 LEU cc_start: 0.6996 (tp) cc_final: 0.6748 (tt)
REVERT: E    3 ILE cc_start: 0.8112 (tp) cc_final: 0.7779 (mt)
REVERT: E  119 GLN cc_start: 0.7205 (tt0) cc_final: 0.6841 (tt0)
REVERT: E  130 SER cc_start: 0.6968 (p) cc_final: 0.6517 (t)
REVERT: E  149 LEU cc_start: 0.8284 (tp) cc_final: 0.7920 (tp)
REVERT: E  150 PHE cc_start: 0.8413 (m-80) cc_final: 0.8026 (m-80)
REVERT: E  171 VAL cc_start: 0.6531 (p) cc_final: 0.6175 (p)
REVERT: G  213 PHE cc_start: 0.8594 (t80) cc_final: 0.8323 (t80)
REVERT: G  265 TYR cc_start: 0.6727 (m-80) cc_final: 0.6272 (m-80)
REVERT: G  296 TYR cc_start: 0.7658 (m-80) cc_final: 0.7092 (m-80)
REVERT: G  369 ILE cc_start: 0.7890 (pt) cc_final: 0.7587 (mt)
REVERT: G  376 TYR cc_start: 0.7129 (t80) cc_final: 0.6843 (t80)
REVERT: G  411 SER cc_start: 0.7740 (t) cc_final: 0.7318 (t)
REVERT: H   26 THR cc_start: 0.6096 (t) cc_final: 0.5867 (t)
REVERT: H   51 GLU cc_start: 0.8537 (pm20) cc_final: 0.8072 (pt0)
REVERT: H  124 MET cc_start: 0.6429 (mtp) cc_final: 0.5940 (mtp)
REVERT: H  148 LEU cc_start: 0.7739 (tp) cc_final: 0.7511 (tp)
REVERT: H  149 LEU cc_start: 0.6738 (mt) cc_final: 0.6274 (mt)
REVERT: Q    7 ASN cc_start: 0.4957 (m110) cc_final: 0.4564 (t0)
REVERT: U   48 LYS cc_start: 0.7588 (tttt) cc_final: 0.7109 (ttpt)
REVERT: U   89 TYR cc_start: 0.6845 (t80) cc_final: 0.6334 (t80)
REVERT: U   91 ASP cc_start: 0.7134 (p0) cc_final: 0.6931 (p0)
REVERT: U   97 LYS cc_start: 0.7451 (ptpt) cc_final: 0.6962 (pttt)
REVERT: U  126 GLN cc_start: 0.6877 (mt0) cc_final: 0.6452 (mm-40)
REVERT: U  127 THR cc_start: 0.7945 (m) cc_final: 0.7396 (p)
REVERT: U  142 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7902 (tm-30)
REVERT: U  143 GLU cc_start: 0.7223 (pt0) cc_final: 0.7017 (pt0)
REVERT: V   38 GLU cc_start: 0.7570 (tt0) cc_final: 0.7212 (tt0)
REVERT: V   49 ASN cc_start: 0.8218 (t0) cc_final: 0.7849 (t0)
REVERT: V   86 LYS cc_start: 0.7676 (mtmm) cc_final: 0.7264 (mtpp)
REVERT: V  141 LEU cc_start: 0.5822 (tp) cc_final: 0.4824 (tp)
REVERT: V  165 LEU cc_start: 0.7719 (tp) cc_final: 0.7451 (tp)
REVERT: W    6 LYS cc_start: 0.7866 (mmpt) cc_final: 0.7625 (mptt)
REVERT: W   11 LEU cc_start: 0.8230 (mt) cc_final: 0.7821 (mt)
REVERT: W   56 LYS cc_start: 0.6349 (ttpp) cc_final: 0.5354 (ptpp)
REVERT: W   59 ASP cc_start: 0.7290 (m-30) cc_final: 0.6978 (m-30)
REVERT: W   68 LEU cc_start: 0.8180 (tp) cc_final: 0.7564 (pt)
REVERT: W   87 ILE cc_start: 0.9322 (mt) cc_final: 0.9074 (mt)
REVERT: W   89 TYR cc_start: 0.7765 (t80) cc_final: 0.7356 (t80)
REVERT: W  151 ASP cc_start: 0.8068 (t0) cc_final: 0.7681 (t0)
REVERT: W  161 MET cc_start: 0.5240 (tpp) cc_final: 0.4613 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 312
  average time/residue: 0.0935
  time to fit residues: 42.4972
Evaluate side-chains
  269 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 269
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 102 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0000
   chunk 36 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 120 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 82 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    1.9390

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  82 ASN
** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 374 GLN
H  38 ASN
Q 136 ASN
** U  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 168 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.136174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.117952 restraints weight = 24296.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.120770 restraints weight = 15116.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.122719 restraints weight = 10426.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.124021 restraints weight = 7811.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.125013 restraints weight = 6266.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.5550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  11418  Z= 0.206
  Angle     :  0.690   7.256  15482  Z= 0.366
  Chirality :  0.048   0.203   1733
  Planarity :  0.005   0.050   1996
  Dihedral  :  5.431  19.901   1527
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.32 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.22), residues: 1379
  helix: -0.39 (0.40), residues: 157
  sheet: -0.28 (0.25), residues: 403
  loop : -0.77 (0.21), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 168 
 TYR   0.029   0.002   TYR E  80 
 PHE   0.022   0.002   PHE G 233 
 TRP   0.010   0.002   TRP E 100 
 HIS   0.006   0.002   HIS G 216 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00477 /  0.21 (11418)
  covalent geometry    : angle       0.68952 /  0.37 (15482)
  hydrogen bonds       : bond        0.04957 /  3.21 (  357)
  hydrogen bonds       : angle       6.54427 /  4.49 (  912)

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

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

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 310
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   25 LEU cc_start: 0.6841 (tp) cc_final: 0.6571 (tt)
REVERT: C   33 TRP cc_start: 0.7266 (m100) cc_final: 0.6652 (m100)
REVERT: E    3 ILE cc_start: 0.8233 (tp) cc_final: 0.7740 (mt)
REVERT: E  119 GLN cc_start: 0.7280 (tt0) cc_final: 0.6833 (tt0)
REVERT: E  130 SER cc_start: 0.7021 (p) cc_final: 0.6553 (t)
REVERT: E  149 LEU cc_start: 0.8321 (tp) cc_final: 0.7939 (tp)
REVERT: E  150 PHE cc_start: 0.8460 (m-80) cc_final: 0.8017 (m-80)
REVERT: E  171 VAL cc_start: 0.6506 (p) cc_final: 0.6187 (p)
REVERT: G  296 TYR cc_start: 0.7781 (m-80) cc_final: 0.7244 (m-80)
REVERT: G  376 TYR cc_start: 0.7197 (t80) cc_final: 0.6813 (t80)
REVERT: G  411 SER cc_start: 0.7773 (t) cc_final: 0.7276 (t)
REVERT: H   51 GLU cc_start: 0.8559 (pm20) cc_final: 0.8169 (pt0)
REVERT: H  148 LEU cc_start: 0.7584 (tp) cc_final: 0.7316 (tp)
REVERT: Q    7 ASN cc_start: 0.4914 (m110) cc_final: 0.4530 (t0)
REVERT: U   48 LYS cc_start: 0.7643 (tttt) cc_final: 0.7128 (ttpt)
REVERT: U   89 TYR cc_start: 0.6803 (t80) cc_final: 0.6345 (t80)
REVERT: U   91 ASP cc_start: 0.7427 (p0) cc_final: 0.7215 (p0)
REVERT: U   97 LYS cc_start: 0.7474 (ptpt) cc_final: 0.6972 (pttt)
REVERT: U  126 GLN cc_start: 0.6842 (mt0) cc_final: 0.6472 (mm-40)
REVERT: U  127 THR cc_start: 0.7932 (m) cc_final: 0.7426 (p)
REVERT: U  142 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7962 (tm-30)
REVERT: V   49 ASN cc_start: 0.8225 (t0) cc_final: 0.7810 (t0)
REVERT: V   86 LYS cc_start: 0.7680 (mtmm) cc_final: 0.7284 (mtpp)
REVERT: V  141 LEU cc_start: 0.5833 (tp) cc_final: 0.4848 (tp)
REVERT: V  159 THR cc_start: 0.7782 (p) cc_final: 0.7445 (p)
REVERT: V  165 LEU cc_start: 0.7798 (tp) cc_final: 0.7410 (tp)
REVERT: V  167 ILE cc_start: 0.8446 (mm) cc_final: 0.8238 (mp)
REVERT: W   11 LEU cc_start: 0.8303 (mt) cc_final: 0.7934 (mt)
REVERT: W   56 LYS cc_start: 0.6250 (ttpp) cc_final: 0.5129 (ptpp)
REVERT: W   57 ASP cc_start: 0.6079 (t0) cc_final: 0.5836 (t0)
REVERT: W   59 ASP cc_start: 0.7291 (m-30) cc_final: 0.6976 (m-30)
REVERT: W   68 LEU cc_start: 0.8261 (tp) cc_final: 0.7584 (pt)
REVERT: W   83 ILE cc_start: 0.7309 (mm) cc_final: 0.6604 (mp)
REVERT: W   89 TYR cc_start: 0.7832 (t80) cc_final: 0.7399 (t80)
REVERT: W  151 ASP cc_start: 0.8095 (t0) cc_final: 0.7819 (t0)
REVERT: W  156 THR cc_start: 0.8301 (m) cc_final: 0.7958 (t)
REVERT: W  161 MET cc_start: 0.5296 (tpp) cc_final: 0.4656 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 311
  average time/residue: 0.0978
  time to fit residues: 44.6360
Evaluate side-chains
  273 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 273
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0370
   chunk 68 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 14 optimal weight:    8.9990
   chunk 7 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 134 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0060
   overall best weight:    0.9478

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 136 ASN
** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 374 GLN
Q 136 ASN
** U  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  72 ASN
W 150 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.140641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.122894 restraints weight = 25077.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.125652 restraints weight = 15679.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.127574 restraints weight = 10840.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.128868 restraints weight = 8127.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.129793 restraints weight = 6512.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7125
moved from start:          0.5599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11418  Z= 0.140
  Angle     :  0.647   9.320  15482  Z= 0.340
  Chirality :  0.047   0.187   1733
  Planarity :  0.005   0.050   1996
  Dihedral  :  5.169  18.482   1527
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.24 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.22), residues: 1379
  helix: -0.25 (0.40), residues: 157
  sheet: -0.05 (0.27), residues: 376
  loop : -0.68 (0.21), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 168 
 TYR   0.031   0.002   TYR E  80 
 PHE   0.018   0.002   PHE Q 169 
 TRP   0.011   0.002   TRP H 100 
 HIS   0.003   0.001   HIS G 216 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.14 (11418)
  covalent geometry    : angle       0.64723 /  0.34 (15482)
  hydrogen bonds       : bond        0.04463 /  2.87 (  357)
  hydrogen bonds       : angle       6.32139 /  4.32 (  912)

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

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

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 308
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   33 TRP cc_start: 0.7245 (m100) cc_final: 0.6621 (m100)
REVERT: C   50 GLN cc_start: 0.7766 (pp30) cc_final: 0.6240 (tp40)
REVERT: E    3 ILE cc_start: 0.7943 (tp) cc_final: 0.7708 (mt)
REVERT: E  118 ARG cc_start: 0.7083 (mtt90) cc_final: 0.6376 (mtt90)
REVERT: E  119 GLN cc_start: 0.7333 (tt0) cc_final: 0.6995 (tt0)
REVERT: E  130 SER cc_start: 0.7004 (p) cc_final: 0.6551 (t)
REVERT: E  149 LEU cc_start: 0.8319 (tp) cc_final: 0.7957 (tp)
REVERT: E  150 PHE cc_start: 0.8415 (m-80) cc_final: 0.7958 (m-80)
REVERT: E  171 VAL cc_start: 0.6492 (p) cc_final: 0.6064 (p)
REVERT: G  296 TYR cc_start: 0.7770 (m-80) cc_final: 0.7214 (m-80)
REVERT: H   51 GLU cc_start: 0.8571 (pm20) cc_final: 0.8061 (pt0)
REVERT: H  118 ARG cc_start: 0.6609 (mtt90) cc_final: 0.6388 (mtt90)
REVERT: H  124 MET cc_start: 0.6762 (mtp) cc_final: 0.6256 (mtp)
REVERT: Q    7 ASN cc_start: 0.4903 (m110) cc_final: 0.4524 (t0)
REVERT: U   48 LYS cc_start: 0.7389 (tttt) cc_final: 0.6930 (ttpt)
REVERT: U   87 ILE cc_start: 0.9099 (mp) cc_final: 0.8883 (mp)
REVERT: U   89 TYR cc_start: 0.6722 (t80) cc_final: 0.6296 (t80)
REVERT: U   91 ASP cc_start: 0.7390 (p0) cc_final: 0.7181 (p0)
REVERT: U   97 LYS cc_start: 0.7407 (ptpt) cc_final: 0.6924 (pttt)
REVERT: U  126 GLN cc_start: 0.7024 (mt0) cc_final: 0.6594 (mm-40)
REVERT: U  127 THR cc_start: 0.7967 (m) cc_final: 0.7391 (p)
REVERT: U  142 GLU cc_start: 0.8225 (tm-30) cc_final: 0.8021 (tm-30)
REVERT: V   32 GLN cc_start: 0.8331 (tp-100) cc_final: 0.8049 (tp-100)
REVERT: V   49 ASN cc_start: 0.8279 (t0) cc_final: 0.7882 (t0)
REVERT: V   86 LYS cc_start: 0.7553 (mtmm) cc_final: 0.7092 (mtpp)
REVERT: V  159 THR cc_start: 0.7760 (p) cc_final: 0.7407 (p)
REVERT: V  165 LEU cc_start: 0.7768 (tp) cc_final: 0.7422 (tp)
REVERT: W   11 LEU cc_start: 0.8212 (mt) cc_final: 0.7800 (mt)
REVERT: W   56 LYS cc_start: 0.6163 (ttpp) cc_final: 0.4981 (mmtt)
REVERT: W   57 ASP cc_start: 0.5942 (t0) cc_final: 0.5702 (t0)
REVERT: W   59 ASP cc_start: 0.7257 (m-30) cc_final: 0.6913 (m-30)
REVERT: W   68 LEU cc_start: 0.8231 (tp) cc_final: 0.7576 (pt)
REVERT: W   83 ILE cc_start: 0.7213 (mm) cc_final: 0.6559 (mp)
REVERT: W   89 TYR cc_start: 0.7738 (t80) cc_final: 0.7315 (t80)
REVERT: W  151 ASP cc_start: 0.8019 (t0) cc_final: 0.7694 (t0)
REVERT: W  156 THR cc_start: 0.8225 (m) cc_final: 0.7781 (t)
REVERT: W  161 MET cc_start: 0.5311 (tpp) cc_final: 0.4666 (tpp)
  outliers start: 2
  outliers final: 0
  residues processed: 309
  average time/residue: 0.0994
  time to fit residues: 45.0082
Evaluate side-chains
  266 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 58 optimal weight:    0.1980
   chunk 115 optimal weight:    0.0970
   chunk 63 optimal weight:    0.5980
   chunk 114 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0980
   chunk 57 optimal weight:    0.9980
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.3778

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 136 ASN
** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 136 ASN
U  26 ASN
** U  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V  33 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.143417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.125492 restraints weight = 24694.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.128415 restraints weight = 15217.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.130395 restraints weight = 10373.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.131796 restraints weight = 7701.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.132622 restraints weight = 6115.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7063
moved from start:          0.5606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11418  Z= 0.118
  Angle     :  0.622   9.388  15482  Z= 0.324
  Chirality :  0.046   0.172   1733
  Planarity :  0.005   0.050   1996
  Dihedral  :  4.820  18.502   1527
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  0.08 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.22), residues: 1379
  helix: -0.17 (0.40), residues: 159
  sheet:  0.20 (0.27), residues: 366
  loop : -0.56 (0.21), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 168 
 TYR   0.033   0.002   TYR E  80 
 PHE   0.019   0.002   PHE H 151 
 TRP   0.036   0.002   TRP H 100 
 HIS   0.002   0.001   HIS G 216 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.12 (11418)
  covalent geometry    : angle       0.62151 /  0.32 (15482)
  hydrogen bonds       : bond        0.04042 /  2.61 (  357)
  hydrogen bonds       : angle       6.04925 /  4.13 (  912)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1883.66 seconds
wall clock time: 33 minutes 24.75 seconds (2004.75 seconds total)