Starting phenix.real_space_refine
on Thu Aug  6 16:30:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rr3_19455/08_2026/8rr3_19455.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rr3_19455/08_2026/8rr3_19455.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rr3_19455/08_2026/8rr3_19455.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rr3_19455/08_2026/8rr3_19455.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rr3_19455/08_2026/8rr3_19455.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rr3_19455/08_2026/8rr3_19455.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.007 sd=   1.089
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P      81      5.49       5
     S      81      5.16       5
     C    9991      2.51       5
     N    2869      2.21       5
     O    3270      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 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: 16294
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 1848
          Classifications: {'peptide': 255}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241}
    Chain: "B"
      Number of atoms: 1622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1622
          Classifications: {'peptide': 226}
          Link IDs: {'PTRANS': 8, 'TRANS': 217}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 1848
          Classifications: {'peptide': 255}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241}
    Chain: "D"
      Number of atoms: 1663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1663
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 5265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 672, 5265
          Classifications: {'peptide': 672}
          Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 631}
          Chain breaks: 3
    Chain: "F"
      Number of atoms: 2278
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2278
          Classifications: {'peptide': 275}
          Link IDs: {'PTRANS': 8, 'TRANS': 266}
          Chain breaks: 1
    Chain: "T"
      Number of atoms: 1742
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 1742
          Classifications: {'RNA': 81}
          Modifications used: {'rna2p_pur': 16, 'rna2p_pyr': 4, 'rna3p_pur': 30, 'rna3p_pyr': 31}
          Link IDs: {'rna2p': 20, 'rna3p': 60}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "F"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Classifications: {'peptide': 1}
  Time building chain proxies: 3.24, per 1000 atoms: 0.20
  Number of scatterers: 16294
  At special positions: 0
  Unit cell: (104.25, 116.76, 166.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      81     16.00
     P      81     15.00
     O    3270      8.00
     N    2869      7.00
     C    9991      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.10
  Conformation dependent library (CDL) restraints added in 695.9 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN E 901 "
        pdb="ZN    ZN E 901 " - pdb=" NE2 HIS E 724 "
        pdb="ZN    ZN E 901 " - pdb=" NE2 HIS E 551 "
      pdb="  ZN E 902 "
        pdb="ZN    ZN E 902 " - pdb=" NE2 HIS E 546 "
        pdb="ZN    ZN E 902 " - pdb=" NE2 HIS E 644 "
        pdb="ZN    ZN E 902 " - pdb=" ND1 HIS E 548 "


  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3482

  Finding SS restraints...
    Secondary structure from input PDB file:
      78 helices and 10 sheets defined
      48.2% alpha, 12.9% beta
      20 base pairs and 33 stacking pairs defined.
    Time for finding SS restraints: 1.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 33
    Processing helix  chain 'A' and resid 46 through 55
    Processing helix  chain 'A' and resid 67 through 83
    Processing helix  chain 'A' and resid 110 through 137
      removed outlier: 3.503A  pdb=" N   PHE A 114 " --> pdb=" O   THR A 110 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   MET A 123 " --> pdb=" O   ASP A 119 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   GLY A 124 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   THR A 125 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   GLY A 134 " --> pdb=" O   ARG A 130 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLU A 135 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 161
    Processing helix  chain 'A' and resid 165 through 187
      removed outlier: 4.557A  pdb=" N   LEU A 180 " --> pdb=" O   VAL A 176 " (cutoff:3.500A)
      Proline residue:  A 181  - end of helix
    Processing helix  chain 'A' and resid 188 through 190
      No H-bonds generated for 'chain 'A' and resid 188 through 190'
    Processing helix  chain 'A' and resid 204 through 209
      removed outlier: 3.590A  pdb=" N   SER A 208 " --> pdb=" O   PRO A 204 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   LEU A 209 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 204 through 209'
    Processing helix  chain 'A' and resid 210 through 220
    Processing helix  chain 'A' and resid 229 through 243
      removed outlier: 3.574A  pdb=" N   TYR A 233 " --> pdb=" O   ASP A 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 33
    Processing helix  chain 'B' and resid 42 through 45
    Processing helix  chain 'B' and resid 46 through 54
      removed outlier: 3.898A  pdb=" N   GLN B  50 " --> pdb=" O   GLY B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 83
      removed outlier: 3.657A  pdb=" N   VAL B  71 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 137
      removed outlier: 3.626A  pdb=" N   PHE B 114 " --> pdb=" O   THR B 110 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLY B 124 " --> pdb=" O   VAL B 120 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLY B 134 " --> pdb=" O   ARG B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 161
    Processing helix  chain 'B' and resid 165 through 187
      removed outlier: 4.419A  pdb=" N   LEU B 180 " --> pdb=" O   VAL B 176 " (cutoff:3.500A)
      Proline residue:  B 181  - end of helix
    Processing helix  chain 'B' and resid 229 through 243
      removed outlier: 3.573A  pdb=" N   TYR B 233 " --> pdb=" O   ASP B 229 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 33
    Processing helix  chain 'C' and resid 46 through 54
      removed outlier: 3.879A  pdb=" N   GLN C  50 " --> pdb=" O   GLY C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 83
      removed outlier: 3.588A  pdb=" N   VAL C  71 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 110 through 137
      removed outlier: 3.739A  pdb=" N   PHE C 114 " --> pdb=" O   THR C 110 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   MET C 123 " --> pdb=" O   ASP C 119 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLY C 124 " --> pdb=" O   VAL C 120 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LEU C 131 " --> pdb=" O   ASN C 127 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 155 through 159
    Processing helix  chain 'C' and resid 165 through 187
      removed outlier: 4.482A  pdb=" N   LEU C 180 " --> pdb=" O   VAL C 176 " (cutoff:3.500A)
      Proline residue:  C 181  - end of helix
    Processing helix  chain 'C' and resid 203 through 208
      removed outlier: 3.594A  pdb=" N   SER C 208 " --> pdb=" O   PRO C 204 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 210 through 221
      removed outlier: 4.004A  pdb=" N   VAL C 221 " --> pdb=" O   LEU C 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 229 through 243
      removed outlier: 3.588A  pdb=" N   TYR C 233 " --> pdb=" O   ASP C 229 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 20 through 33
    Processing helix  chain 'D' and resid 46 through 54
      removed outlier: 3.961A  pdb=" N   GLN D  50 " --> pdb=" O   GLY D  46 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 82
    Processing helix  chain 'D' and resid 110 through 137
      removed outlier: 3.521A  pdb=" N   PHE D 114 " --> pdb=" O   THR D 110 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   MET D 123 " --> pdb=" O   ASP D 119 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   GLY D 124 " --> pdb=" O   VAL D 120 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   THR D 125 " --> pdb=" O   ASN D 121 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLY D 134 " --> pdb=" O   ARG D 130 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 155 through 159
    Processing helix  chain 'D' and resid 165 through 187
      removed outlier: 4.448A  pdb=" N   LEU D 180 " --> pdb=" O   VAL D 176 " (cutoff:3.500A)
      Proline residue:  D 181  - end of helix
    Processing helix  chain 'D' and resid 229 through 243
      removed outlier: 3.734A  pdb=" N   TYR D 233 " --> pdb=" O   ASP D 229 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 98
    Processing helix  chain 'E' and resid 114 through 119
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'E' and resid 143 through 152
      removed outlier: 3.618A  pdb=" N   LYS E 152 " --> pdb=" O   LEU E 148 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 258 through 263
      removed outlier: 4.132A  pdb=" N   MET E 262 " --> pdb=" O   LYS E 258 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 270 through 280
      removed outlier: 4.374A  pdb=" N   ILE E 274 " --> pdb=" O   ALA E 270 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 292 through 296
    Processing helix  chain 'E' and resid 313 through 315
      No H-bonds generated for 'chain 'E' and resid 313 through 315'
    Processing helix  chain 'E' and resid 316 through 323
    Processing helix  chain 'E' and resid 323 through 331
      removed outlier: 3.806A  pdb=" N   GLN E 327 " --> pdb=" O   ASN E 323 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   TYR E 329 " --> pdb=" O   THR E 325 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 345 through 350
      removed outlier: 3.529A  pdb=" N   LEU E 349 " --> pdb=" O   PRO E 345 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 351 through 360
      removed outlier: 3.503A  pdb=" N   GLU E 359 " --> pdb=" O   GLN E 355 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 379 through 391
      removed outlier: 3.743A  pdb=" N   LEU E 391 " --> pdb=" O   THR E 387 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 442 through 452
      removed outlier: 3.564A  pdb=" N   PHE E 446 " --> pdb=" O   ASN E 442 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 455 through 467
      removed outlier: 3.713A  pdb=" N   SER E 459 " --> pdb=" O   ASN E 455 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   ALA E 467 " --> pdb=" O   TYR E 463 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 519 through 529
    Processing helix  chain 'E' and resid 531 through 538
    Processing helix  chain 'E' and resid 554 through 570
      removed outlier: 3.513A  pdb=" N   ILE E 558 " --> pdb=" O   GLY E 554 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 582 through 595
      removed outlier: 4.055A  pdb=" N   ALA E 586 " --> pdb=" O   ASN E 582 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   TRP E 587 " --> pdb=" O   GLN E 583 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 598 through 600
      No H-bonds generated for 'chain 'E' and resid 598 through 600'
    Processing helix  chain 'E' and resid 608 through 611
    Processing helix  chain 'E' and resid 618 through 632
    Processing helix  chain 'E' and resid 670 through 677
      removed outlier: 3.813A  pdb=" N   VAL E 674 " --> pdb=" O   CYS E 670 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 690 through 692
      No H-bonds generated for 'chain 'E' and resid 690 through 692'
    Processing helix  chain 'E' and resid 693 through 700
    Processing helix  chain 'E' and resid 704 through 716
    Processing helix  chain 'E' and resid 755 through 757
      No H-bonds generated for 'chain 'E' and resid 755 through 757'
    Processing helix  chain 'E' and resid 759 through 762
    Processing helix  chain 'E' and resid 763 through 771
    Processing helix  chain 'E' and resid 771 through 792
    Processing helix  chain 'F' and resid 93 through 104
    Processing helix  chain 'F' and resid 113 through 121
    Processing helix  chain 'F' and resid 125 through 154
    Processing helix  chain 'F' and resid 183 through 202
      removed outlier: 3.596A  pdb=" N   MET F 187 " --> pdb=" O   TRP F 183 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   GLN F 200 " --> pdb=" O   ALA F 196 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 210 through 215
      removed outlier: 4.258A  pdb=" N   ASN F 213 " --> pdb=" O   ALA F 210 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   MET F 215 " --> pdb=" O   GLU F 212 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 216 through 237
    Processing helix  chain 'F' and resid 252 through 263
    Processing helix  chain 'F' and resid 264 through 269
      removed outlier: 3.837A  pdb=" N   ASP F 267 " --> pdb=" O   GLU F 264 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU F 269 " --> pdb=" O   TRP F 266 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 277 through 281
    Processing helix  chain 'F' and resid 320 through 329
      removed outlier: 3.613A  pdb=" N   LEU F 329 " --> pdb=" O   LYS F 325 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 352 through 365
    Processing helix  chain 'F' and resid 368 through 373
    Processing helix  chain 'F' and resid 374 through 376
      No H-bonds generated for 'chain 'F' and resid 374 through 376'
    Processing helix  chain 'F' and resid 377 through 381
    Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 62
      removed outlier: 6.750A  pdb=" N   ALA A  37 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   ALA A  61 " --> pdb=" O   ALA A  37 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   LEU A  39 " --> pdb=" O   ALA A  61 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ALA A  88 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 8.263A  pdb=" N   THR A 153 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   ASN A  90 " --> pdb=" O   THR A 153 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 6.343A  pdb=" N   ALA B  88 " --> pdb=" O   ILE B 151 " (cutoff:3.500A)
      removed outlier: 8.096A  pdb=" N   THR B 153 " --> pdb=" O   ALA B  88 " (cutoff:3.500A)
      removed outlier: 7.558A  pdb=" N   ASN B  90 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   GLU B 249 " --> pdb=" O   VAL B 193 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 62
      removed outlier: 6.850A  pdb=" N   ALA C  37 " --> pdb=" O   VAL C  59 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   ALA C  61 " --> pdb=" O   ALA C  37 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LEU C  39 " --> pdb=" O   ALA C  61 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 58 through 62
      removed outlier: 6.621A  pdb=" N   ALA D  37 " --> pdb=" O   VAL D  59 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   ALA D  61 " --> pdb=" O   ALA D  37 " (cutoff:3.500A)
      removed outlier: 6.019A  pdb=" N   LEU D  39 " --> pdb=" O   ALA D  61 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR D 153 " --> pdb=" O   ASN D  90 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 162 through 167
      removed outlier: 6.477A  pdb=" N   ARG E  82 " --> pdb=" O   ASN E 107 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   PHE E 109 " --> pdb=" O   ARG E  82 " (cutoff:3.500A)
      removed outlier: 5.960A  pdb=" N   LEU E  84 " --> pdb=" O   PHE E 109 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ALA E  73 " --> pdb=" O   VAL E  63 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   LEU E 423 " --> pdb=" O   VAL E  62 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   LYS E 424 " --> pdb=" O   GLN E 434 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   GLN E 434 " --> pdb=" O   LYS E 424 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 173 through 174
      removed outlier: 6.187A  pdb=" N   VAL E 241 " --> pdb=" O   GLU E 310 " (cutoff:3.500A)
      removed outlier: 5.379A  pdb=" N   GLU E 310 " --> pdb=" O   VAL E 241 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 602 through 606
      removed outlier: 6.476A  pdb=" N   LEU E 576 " --> pdb=" O   SER E 603 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   ILE E 605 " --> pdb=" O   LEU E 576 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   VAL E 578 " --> pdb=" O   ILE E 605 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   ALA E 540 " --> pdb=" O   LEU E 577 " (cutoff:3.500A)
      removed outlier: 8.076A  pdb=" N   VAL E 579 " --> pdb=" O   ALA E 540 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   VAL E 542 " --> pdb=" O   VAL E 579 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   SER E 511 " --> pdb=" O   ALA E 541 " (cutoff:3.500A)
      removed outlier: 8.496A  pdb=" N   PHE E 543 " --> pdb=" O   SER E 511 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LEU E 513 " --> pdb=" O   PHE E 543 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   THR E 510 " --> pdb=" O   ILE E 506 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE E 506 " --> pdb=" O   THR E 510 " (cutoff:3.500A)
      removed outlier: 5.958A  pdb=" N   THR E 502 " --> pdb=" O   LEU E 514 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   ALA E 501 " --> pdb=" O   LEU E 486 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LEU E 486 " --> pdb=" O   ALA E 501 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   MET E 750 " --> pdb=" O   PHE E 485 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 636 through 638
      removed outlier: 3.530A  pdb=" N   GLU E 636 " --> pdb=" O   VAL E 654 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   VAL E 654 " --> pdb=" O   GLU E 636 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   LYS E 660 " --> pdb=" O   LEU E 682 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   ILE E 684 " --> pdb=" O   LYS E 660 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   VAL E 662 " --> pdb=" O   ILE E 684 " (cutoff:3.500A)
      removed outlier: 8.541A  pdb=" N   GLU E 686 " --> pdb=" O   VAL E 662 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 272 through 273
      removed outlier: 8.515A  pdb=" N   ILE F 309 " --> pdb=" O   PRO F 204 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   VAL F 206 " --> pdb=" O   ILE F 309 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   ILE F 288 " --> pdb=" O   VAL F 308 " (cutoff:3.500A)
      removed outlier: 8.091A  pdb=" N   GLY F 310 " --> pdb=" O   ILE F 288 " (cutoff:3.500A)
      removed outlier: 8.945A  pdb=" N   LEU F 290 " --> pdb=" O   GLY F 310 " (cutoff:3.500A)

    703 hydrogen bonds defined for protein.
    2025 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      51 hydrogen bonds
      90 hydrogen bond angles
      0 basepair planarities
      20 basepair parallelities
      33 stacking parallelities
  Total time for adding SS restraints: 3.01

  Time building geometry restraints manager: 1.49 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3258
        1.33 -     1.45: 4023
        1.45 -     1.57: 9183
        1.57 -     1.69: 159
        1.69 -     1.81: 129
  Bond restraints: 16752
  Sorted by residual:
  bond pdb=" C2  SAH F 501 "
       pdb=" N3  SAH F 501 "
    ideal  model  delta    sigma   weight residual
    1.322  1.380 -0.058 2.00e-02 2.50e+03 8.47e+00
  bond pdb=" N   ILE F  98 "
       pdb=" CA  ILE F  98 "
    ideal  model  delta    sigma   weight residual
    1.460  1.491 -0.032 1.21e-02 6.83e+03 6.88e+00
  bond pdb=" N   LEU F 342 "
       pdb=" CA  LEU F 342 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.16e-02 7.43e+03 6.84e+00
  bond pdb=" N   LEU F 351 "
       pdb=" CA  LEU F 351 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.032 1.21e-02 6.83e+03 6.78e+00
  bond pdb=" C8  SAH F 501 "
       pdb=" N7  SAH F 501 "
    ideal  model  delta    sigma   weight residual
    1.299  1.350 -0.051 2.00e-02 2.50e+03 6.41e+00
  ... (remaining 16747 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.67: 22547
        2.67 -     5.35: 464
        5.35 -     8.02: 48
        8.02 -    10.69: 16
       10.69 -    13.36: 2
  Bond angle restraints: 23077
  Sorted by residual:
  angle pdb=" N   LEU A 205 "
        pdb=" CA  LEU A 205 "
        pdb=" C   LEU A 205 "
      ideal   model   delta    sigma   weight residual
     111.71  106.10    5.61 1.15e+00 7.56e-01 2.38e+01
  angle pdb=" O4'   G T  19 "
        pdb=" C1'   G T  19 "
        pdb=" N9    G T  19 "
      ideal   model   delta    sigma   weight residual
     108.20  104.33    3.87 8.00e-01 1.56e+00 2.34e+01
  angle pdb=" C1'   G T  73 "
        pdb=" N9    G T  73 "
        pdb=" C4    G T  73 "
      ideal   model   delta    sigma   weight residual
     126.50  132.37   -5.87 1.30e+00 5.92e-01 2.04e+01
  angle pdb=" CB  MET E 721 "
        pdb=" CG  MET E 721 "
        pdb=" SD  MET E 721 "
      ideal   model   delta    sigma   weight residual
     112.70  126.06  -13.36 3.00e+00 1.11e-01 1.98e+01
  angle pdb=" O2    U T   1 "
        pdb=" C2    U T   1 "
        pdb=" N3    U T   1 "
      ideal   model   delta    sigma   weight residual
     122.20  119.13    3.07 7.00e-01 2.04e+00 1.92e+01
  ... (remaining 23072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.47: 9777
       35.47 -    70.94: 404
       70.94 -   106.40: 40
      106.40 -   141.87: 3
      141.87 -   177.34: 3
  Dihedral angle restraints: 10227
    sinusoidal: 4807
      harmonic: 5420
  Sorted by residual:
  dihedral pdb=" CA  SER F 316 "
           pdb=" C   SER F 316 "
           pdb=" N   MET F 317 "
           pdb=" CA  MET F 317 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.86  -24.14     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" C4'   U T   1 "
           pdb=" C3'   U T   1 "
           pdb=" O3'   U T   1 "
           pdb=" P     A T   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   42.66  177.34     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'   A T  15 "
           pdb=" C3'   A T  15 "
           pdb=" O3'   A T  15 "
           pdb=" P     U T  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -110.00   66.47 -176.47     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 10224 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1853
       0.044 -    0.089: 543
       0.089 -    0.133: 239
       0.133 -    0.177: 67
       0.177 -    0.222: 12
  Chirality restraints: 2714
  Sorted by residual:
  chirality pdb=" CA  ILE F 346 "
            pdb=" N   ILE F 346 "
            pdb=" C   ILE F 346 "
            pdb=" CB  ILE F 346 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" C1'   U T   6 "
            pdb=" O4'   U T   6 "
            pdb=" C2'   U T   6 "
            pdb=" N1    U T   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.25    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  PHE A 201 "
            pdb=" N   PHE A 201 "
            pdb=" C   PHE A 201 "
            pdb=" CB  PHE A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.08e+00
  ... (remaining 2711 not shown)

  Planarity restraints: 2693
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E  77 "    0.023 2.00e-02 2.50e+03   2.48e-02 1.07e+01
        pdb=" CG  PHE E  77 "   -0.058 2.00e-02 2.50e+03
        pdb=" CD1 PHE E  77 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE E  77 "    0.017 2.00e-02 2.50e+03
        pdb=" CE1 PHE E  77 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE E  77 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE E  77 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP C 113 "    0.013 2.00e-02 2.50e+03   2.69e-02 7.24e+00
        pdb=" C   ASP C 113 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   ASP C 113 "    0.017 2.00e-02 2.50e+03
        pdb=" N   PHE C 114 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG C 130 "   -0.012 2.00e-02 2.50e+03   2.36e-02 5.59e+00
        pdb=" C   ARG C 130 "    0.041 2.00e-02 2.50e+03
        pdb=" O   ARG C 130 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LEU C 131 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 2690 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 211
        2.61 -     3.19: 14342
        3.19 -     3.76: 26171
        3.76 -     4.33: 35674
        4.33 -     4.90: 57508
  Nonbonded interactions: 133906
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP E 666 "
            pdb="ZN    ZN E 901 "
     model   vdw
     2.042 2.230
  nonbonded pdb=" OD1 ASP E 691 "
            pdb=" OG  SER E 706 "
     model   vdw
     2.088 3.040
  nonbonded pdb=" OD2 ASP E 666 "
            pdb="ZN    ZN E 901 "
     model   vdw
     2.115 2.230
  nonbonded pdb=" OD1 ASN F 222 "
            pdb=" O2'   G T   9 "
     model   vdw
     2.136 3.040
  nonbonded pdb=" O   LEU F 290 "
            pdb=" O2' SAH F 501 "
     model   vdw
     2.152 3.040
  ... (remaining 133901 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 8 through 103 or resid 107 through 202 or resid 225 throug \ 
h 257))
  selection = (chain 'B' and resid 8 through 257)
  selection = (chain 'C' and (resid 8 through 103 or resid 107 through 202 or resid 225 throug \ 
h 257))
  selection = (chain 'D' and (resid 8 through 103 or resid 107 through 202 or resid 225 throug \ 
h 257))
}

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=0.87 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     17.530
  Find NCS groups from input model:        0.180
  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:             0.010
  Load rotamer database and sin/cos tables:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.246  16757  Z= 0.221
  Angle     :  0.910  13.363  23077  Z= 0.546
  Chirality :  0.054   0.222   2714
  Planarity :  0.005   0.040   2693
  Dihedral  : 18.124 177.340   6745
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.97 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 15.16 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.40 %
    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:  0.53 (0.20), residues: 1888
  helix:  1.18 (0.18), residues: 777
  sheet:  0.16 (0.29), residues: 330
  loop : -0.31 (0.24), residues: 781

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 130 
 TYR   0.039   0.003   TYR B 233 
 PHE   0.058   0.002   PHE E  77 
 TRP   0.014   0.002   TRP E 433 
 HIS   0.008   0.001   HIS E 644 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.19 (16752)
  covalent geometry    : angle       0.90999 /  0.55 (23077)
  hydrogen bonds       : bond        0.17599 / 11.95 (  754)
  hydrogen bonds       : angle       7.24120 /  5.12 ( 2115)
  metal coordination   : bond        0.18120 / 12.79 (    5)

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

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

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 216
  time to evaluate  : 0.589 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  257 ILE cc_start: 0.7136 (tp) cc_final: 0.6558 (pt)
REVERT: E  518 GLU cc_start: 0.7655 (pt0) cc_final: 0.6947 (pp20)
REVERT: E  552 HIS cc_start: 0.8454 (p-80) cc_final: 0.8170 (p-80)
REVERT: F  187 MET cc_start: 0.7512 (mtt) cc_final: 0.7272 (mtt)
REVERT: F  188 ASP cc_start: 0.7389 (m-30) cc_final: 0.6902 (m-30)
  outliers start: 9
  outliers final: 3
  residues processed: 220
  average time/residue: 0.1248
  time to fit residues: 40.7089
Evaluate side-chains
  179 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 176
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  100 MET
Chi-restraints excluded: chain F residue  108 VAL
Chi-restraints excluded: chain F residue  346 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 194 optimal weight:    9.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.2980
   chunk 103 optimal weight:    0.0010
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    0.0070
   overall best weight:    0.4608

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  90 ASN
A 115 GLN
A 139 ASN
C 107 GLN
D 115 GLN
E  56 ASN
E 107 ASN
** E 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 176 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.140996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.114714 restraints weight = 35210.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3763 rms_B_bonded: 2.50
r_work: 0.3629 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3638
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3638 r_free = 0.3638    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3638 r_free = 0.3638    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (9 function evaluations)
r_final: 0.3638
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.1107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  16757  Z= 0.137
  Angle     :  0.636   8.485  23077  Z= 0.333
  Chirality :  0.045   0.300   2714
  Planarity :  0.005   0.044   2693
  Dihedral  : 17.480 177.712   3319
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.41 %
    Favored  : 84.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.40 %
    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:  1.03 (0.20), residues: 1888
  helix:  1.70 (0.18), residues: 793
  sheet:  0.16 (0.29), residues: 319
  loop : -0.05 (0.24), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 130 
 TYR   0.014   0.002   TYR E  59 
 PHE   0.017   0.002   PHE A 245 
 TRP   0.010   0.001   TRP E 433 
 HIS   0.005   0.001   HIS E 724 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.14 (16752)
  covalent geometry    : angle       0.63604 /  0.33 (23077)
  hydrogen bonds       : bond        0.05167 /  3.51 (  754)
  hydrogen bonds       : angle       5.38402 /  3.82 ( 2115)
  metal coordination   : bond        0.00684 /  0.42 (    5)

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

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

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 198
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 ARG cc_start: 0.6738 (mtm110) cc_final: 0.6400 (mtp85)
REVERT: B  111 LEU cc_start: 0.8511 (tp) cc_final: 0.8286 (tp)
REVERT: B  233 TYR cc_start: 0.8075 (t80) cc_final: 0.7764 (t80)
REVERT: C   41 ASP cc_start: 0.7797 (t70) cc_final: 0.7562 (t70)
REVERT: C  189 ILE cc_start: 0.8724 (mm) cc_final: 0.8344 (tt)
REVERT: D   60 PHE cc_start: 0.7433 (t80) cc_final: 0.7219 (t80)
REVERT: E  151 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7899 (mm)
REVERT: E  301 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7135 (p0)
REVERT: F  188 ASP cc_start: 0.7877 (m-30) cc_final: 0.7488 (m-30)
  outliers start: 29
  outliers final: 6
  residues processed: 216
  average time/residue: 0.1067
  time to fit residues: 35.2658
Evaluate side-chains
  175 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 167
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   67 SER
Chi-restraints excluded: chain E residue  128 LEU
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  301 ASP
Chi-restraints excluded: chain E residue  503 LEU
Chi-restraints excluded: chain F residue  123 CYS
Chi-restraints excluded: chain F residue  297 VAL
Chi-restraints excluded: chain F residue  346 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 148 optimal weight:    0.4980
   chunk 107 optimal weight:    0.0980
   chunk 94 optimal weight:    3.9990
   chunk 119 optimal weight:    5.9990
   chunk 140 optimal weight:    5.9990
   chunk 152 optimal weight:    7.9990
   chunk 83 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   chunk 91 optimal weight:    0.5980
   chunk 164 optimal weight:    0.0980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 107 ASN
** E 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.140932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.114371 restraints weight = 35523.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 2.65
r_work: 0.3616 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.1492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  16757  Z= 0.118
  Angle     :  0.577   8.496  23077  Z= 0.299
  Chirality :  0.043   0.293   2714
  Planarity :  0.004   0.043   2693
  Dihedral  : 17.387 178.164   3315
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.38 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.40 %
    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:  1.12 (0.20), residues: 1888
  helix:  1.74 (0.18), residues: 801
  sheet:  0.19 (0.29), residues: 333
  loop :  0.02 (0.24), residues: 754

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E  82 
 TYR   0.023   0.002   TYR D 101 
 PHE   0.018   0.001   PHE E 109 
 TRP   0.020   0.001   TRP F 101 
 HIS   0.005   0.001   HIS E 551 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.12 (16752)
  covalent geometry    : angle       0.57704 /  0.30 (23077)
  hydrogen bonds       : bond        0.04478 /  3.04 (  754)
  hydrogen bonds       : angle       5.02691 /  3.55 ( 2115)
  metal coordination   : bond        0.00192 /  0.10 (    5)

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

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

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 190
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  112 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6794 (mp0)
REVERT: B  233 TYR cc_start: 0.8109 (t80) cc_final: 0.7812 (t80)
REVERT: C   41 ASP cc_start: 0.7931 (t70) cc_final: 0.7605 (t70)
REVERT: C  142 ASP cc_start: 0.6529 (t0) cc_final: 0.6285 (t0)
REVERT: C  189 ILE cc_start: 0.8713 (mm) cc_final: 0.8387 (tt)
REVERT: D   28 GLU cc_start: 0.8565 (pt0) cc_final: 0.8332 (pt0)
REVERT: D   60 PHE cc_start: 0.7342 (t80) cc_final: 0.7132 (t80)
REVERT: E  151 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7827 (mm)
REVERT: F  188 ASP cc_start: 0.7880 (m-30) cc_final: 0.7465 (m-30)
  outliers start: 33
  outliers final: 20
  residues processed: 211
  average time/residue: 0.1249
  time to fit residues: 39.5080
Evaluate side-chains
  184 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 163
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  113 ASP
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue   39 LEU
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain E residue  122 SER
Chi-restraints excluded: chain E residue  128 LEU
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  257 LEU
Chi-restraints excluded: chain E residue  503 LEU
Chi-restraints excluded: chain E residue  525 CYS
Chi-restraints excluded: chain E residue  551 HIS
Chi-restraints excluded: chain E residue  634 LEU
Chi-restraints excluded: chain E residue  689 LEU
Chi-restraints excluded: chain E residue  745 VAL
Chi-restraints excluded: chain E residue  780 GLU
Chi-restraints excluded: chain F residue  123 CYS
Chi-restraints excluded: chain F residue  297 VAL
Chi-restraints excluded: chain F residue  346 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks:
   chunk 195 optimal weight:   10.0000
   chunk 126 optimal weight:    8.9990
   chunk 107 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 162 optimal weight:    8.9990
   chunk 21 optimal weight:    0.8980
   chunk 113 optimal weight:    0.0050
   chunk 150 optimal weight:    6.9990
   chunk 28 optimal weight:    0.0070
   chunk 103 optimal weight:    0.8980
   chunk 60 optimal weight:    6.9990
   overall best weight:    0.7614

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  56 ASN
C 260 GLN
** E 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.138278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.110441 restraints weight = 35182.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 2.75
r_work: 0.3538 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.1772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  16757  Z= 0.120
  Angle     :  0.564   9.624  23077  Z= 0.291
  Chirality :  0.043   0.297   2714
  Planarity :  0.004   0.046   2693
  Dihedral  : 17.361 179.856   3315
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.44 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.40 %
    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:  1.09 (0.20), residues: 1888
  helix:  1.77 (0.18), residues: 803
  sheet:  0.11 (0.28), residues: 333
  loop : -0.03 (0.24), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  82 
 TYR   0.023   0.002   TYR E  59 
 PHE   0.022   0.001   PHE A 245 
 TRP   0.007   0.001   TRP E 115 
 HIS   0.005   0.001   HIS E 749 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.12 (16752)
  covalent geometry    : angle       0.56423 /  0.29 (23077)
  hydrogen bonds       : bond        0.04164 /  2.82 (  754)
  hydrogen bonds       : angle       4.90811 /  3.47 ( 2115)
  metal coordination   : bond        0.00138 /  0.07 (    5)

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

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

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 172
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 ASN cc_start: 0.7121 (m-40) cc_final: 0.6728 (m110)
REVERT: B  112 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6897 (mp0)
REVERT: B  168 TYR cc_start: 0.6946 (t80) cc_final: 0.6362 (t80)
REVERT: B  233 TYR cc_start: 0.8126 (t80) cc_final: 0.7844 (t80)
REVERT: C   41 ASP cc_start: 0.8041 (t70) cc_final: 0.7652 (t70)
REVERT: C  189 ILE cc_start: 0.8682 (mm) cc_final: 0.8387 (tt)
REVERT: D   28 GLU cc_start: 0.8577 (pt0) cc_final: 0.8325 (pt0)
REVERT: D   60 PHE cc_start: 0.7508 (t80) cc_final: 0.7186 (t80)
REVERT: E  151 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7841 (mm)
REVERT: E  301 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.7154 (p0)
  outliers start: 33
  outliers final: 19
  residues processed: 195
  average time/residue: 0.1114
  time to fit residues: 33.2701
Evaluate side-chains
  182 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 161
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain E residue  122 SER
Chi-restraints excluded: chain E residue  128 LEU
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  257 LEU
Chi-restraints excluded: chain E residue  301 ASP
Chi-restraints excluded: chain E residue  432 GLU
Chi-restraints excluded: chain E residue  486 LEU
Chi-restraints excluded: chain E residue  503 LEU
Chi-restraints excluded: chain E residue  525 CYS
Chi-restraints excluded: chain E residue  634 LEU
Chi-restraints excluded: chain E residue  642 VAL
Chi-restraints excluded: chain E residue  689 LEU
Chi-restraints excluded: chain E residue  745 VAL
Chi-restraints excluded: chain E residue  776 GLU
Chi-restraints excluded: chain F residue  123 CYS
Chi-restraints excluded: chain F residue  274 THR
Chi-restraints excluded: chain F residue  297 VAL
Chi-restraints excluded: chain F residue  346 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0470
   chunk 29 optimal weight:    0.0170
   chunk 93 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 176 optimal weight:    2.9990
   chunk 139 optimal weight:    2.9990
   chunk 163 optimal weight:    0.0170
   overall best weight:    0.3754

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  56 ASN
** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.138953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.111596 restraints weight = 34966.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 2.78
r_work: 0.3551 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  16757  Z= 0.103
  Angle     :  0.552   9.419  23077  Z= 0.283
  Chirality :  0.042   0.300   2714
  Planarity :  0.004   0.045   2693
  Dihedral  : 17.316 178.339   3315
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 14.70 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.40 %
    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:  1.13 (0.20), residues: 1888
  helix:  1.84 (0.18), residues: 802
  sheet:  0.10 (0.28), residues: 335
  loop : -0.03 (0.24), residues: 751

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E  82 
 TYR   0.026   0.002   TYR D 101 
 PHE   0.014   0.001   PHE A 245 
 TRP   0.006   0.001   TRP E 115 
 HIS   0.006   0.001   HIS E 527 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00212 /  0.10 (16752)
  covalent geometry    : angle       0.55238 /  0.28 (23077)
  hydrogen bonds       : bond        0.03904 /  2.66 (  754)
  hydrogen bonds       : angle       4.77621 /  3.37 ( 2115)
  metal coordination   : bond        0.00047 /  0.03 (    5)

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

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

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 185
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 LYS cc_start: 0.8507 (tptp) cc_final: 0.7784 (mtmt)
REVERT: B  110 THR cc_start: 0.8152 (t) cc_final: 0.7546 (t)
REVERT: B  112 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7103 (mp0)
REVERT: B  168 TYR cc_start: 0.6848 (t80) cc_final: 0.6256 (t80)
REVERT: B  257 ILE cc_start: 0.7388 (tp) cc_final: 0.6940 (pt)
REVERT: C   29 ARG cc_start: 0.6657 (ttt90) cc_final: 0.6364 (ttt180)
REVERT: C   41 ASP cc_start: 0.8019 (t70) cc_final: 0.7622 (t70)
REVERT: C  189 ILE cc_start: 0.8628 (mm) cc_final: 0.8358 (tt)
REVERT: D   28 GLU cc_start: 0.8566 (pt0) cc_final: 0.8330 (pt0)
REVERT: D   60 PHE cc_start: 0.7475 (t80) cc_final: 0.7224 (t80)
REVERT: E  151 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7844 (mm)
REVERT: E  183 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.7854 (tp)
REVERT: E  750 MET cc_start: 0.7995 (tpp) cc_final: 0.7792 (tpp)
  outliers start: 29
  outliers final: 18
  residues processed: 203
  average time/residue: 0.1189
  time to fit residues: 36.6267
Evaluate side-chains
  185 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 165
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain D residue   67 SER
Chi-restraints excluded: chain E residue  122 SER
Chi-restraints excluded: chain E residue  128 LEU
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain E residue  257 LEU
Chi-restraints excluded: chain E residue  432 GLU
Chi-restraints excluded: chain E residue  486 LEU
Chi-restraints excluded: chain E residue  503 LEU
Chi-restraints excluded: chain E residue  621 VAL
Chi-restraints excluded: chain E residue  642 VAL
Chi-restraints excluded: chain E residue  689 LEU
Chi-restraints excluded: chain E residue  745 VAL
Chi-restraints excluded: chain E residue  776 GLU
Chi-restraints excluded: chain F residue  123 CYS
Chi-restraints excluded: chain F residue  297 VAL
Chi-restraints excluded: chain F residue  346 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 168 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 87 optimal weight:    6.9990
   chunk 186 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 172 optimal weight:    0.1980
   chunk 162 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   chunk 121 optimal weight:    3.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  61 GLN
** E 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.136757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.109260 restraints weight = 34842.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 2.59
r_work: 0.3512 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.2170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  16757  Z= 0.128
  Angle     :  0.575  10.568  23077  Z= 0.293
  Chirality :  0.043   0.298   2714
  Planarity :  0.004   0.050   2693
  Dihedral  : 17.293 179.347   3315
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 15.16 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.40 %
    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:  1.10 (0.20), residues: 1888
  helix:  1.82 (0.18), residues: 803
  sheet:  0.05 (0.28), residues: 335
  loop : -0.06 (0.24), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  84 
 TYR   0.026   0.002   TYR D 101 
 PHE   0.027   0.001   PHE B 114 
 TRP   0.008   0.001   TRP E 115 
 HIS   0.004   0.001   HIS E 168 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.13 (16752)
  covalent geometry    : angle       0.57529 /  0.29 (23077)
  hydrogen bonds       : bond        0.03975 /  2.70 (  754)
  hydrogen bonds       : angle       4.79447 /  3.39 ( 2115)
  metal coordination   : bond        0.00181 /  0.10 (    5)

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

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

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 177
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  110 THR cc_start: 0.8223 (t) cc_final: 0.7583 (t)
REVERT: B  233 TYR cc_start: 0.8147 (t80) cc_final: 0.7846 (t80)
REVERT: B  257 ILE cc_start: 0.7471 (tp) cc_final: 0.7039 (pt)
REVERT: C   41 ASP cc_start: 0.8075 (t70) cc_final: 0.7623 (t70)
REVERT: C  189 ILE cc_start: 0.8670 (mm) cc_final: 0.8380 (tt)
REVERT: D   28 GLU cc_start: 0.8536 (pt0) cc_final: 0.8287 (pt0)
REVERT: E  151 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7815 (mm)
REVERT: E  301 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7169 (p0)
REVERT: E  750 MET cc_start: 0.8137 (tpp) cc_final: 0.7843 (tpp)
REVERT: F  184 ASP cc_start: 0.7643 (t0) cc_final: 0.6928 (t0)
REVERT: F  188 ASP cc_start: 0.7966 (m-30) cc_final: 0.7337 (m-30)
  outliers start: 35
  outliers final: 23
  residues processed: 200
  average time/residue: 0.1107
  time to fit residues: 34.0433
Evaluate side-chains
  188 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 163
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain D residue   67 SER
Chi-restraints excluded: chain E residue  122 SER
Chi-restraints excluded: chain E residue  128 LEU
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain E residue  257 LEU
Chi-restraints excluded: chain E residue  301 ASP
Chi-restraints excluded: chain E residue  432 GLU
Chi-restraints excluded: chain E residue  486 LEU
Chi-restraints excluded: chain E residue  488 THR
Chi-restraints excluded: chain E residue  503 LEU
Chi-restraints excluded: chain E residue  525 CYS
Chi-restraints excluded: chain E residue  551 HIS
Chi-restraints excluded: chain E residue  555 LEU
Chi-restraints excluded: chain E residue  628 LEU
Chi-restraints excluded: chain E residue  642 VAL
Chi-restraints excluded: chain E residue  689 LEU
Chi-restraints excluded: chain E residue  745 VAL
Chi-restraints excluded: chain E residue  776 GLU
Chi-restraints excluded: chain F residue  123 CYS
Chi-restraints excluded: chain F residue  346 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks:
   chunk 180 optimal weight:    6.9990
   chunk 46 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 131 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 116 optimal weight:    0.9980
   chunk 163 optimal weight:    0.0070
   chunk 156 optimal weight:    0.1980
   chunk 194 optimal weight:   10.0000
   overall best weight:    0.8402

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E 551 HIS ** 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 = 0.4082 r_free = 0.4082 target = 0.136742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.109452 restraints weight = 34815.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 2.53
r_work: 0.3515 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  16757  Z= 0.120
  Angle     :  0.566  10.649  23077  Z= 0.289
  Chirality :  0.043   0.300   2714
  Planarity :  0.004   0.052   2693
  Dihedral  : 17.269 179.093   3315
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 15.41 %
    Favored  : 82.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.40 %
    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:  1.08 (0.20), residues: 1888
  helix:  1.84 (0.18), residues: 802
  sheet:  0.06 (0.28), residues: 347
  loop : -0.13 (0.24), residues: 739

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  82 
 TYR   0.025   0.002   TYR D 101 
 PHE   0.024   0.001   PHE B 114 
 TRP   0.006   0.001   TRP E 115 
 HIS   0.003   0.001   HIS F 381 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 (16752)
  covalent geometry    : angle       0.56559 /  0.29 (23077)
  hydrogen bonds       : bond        0.03853 /  2.62 (  754)
  hydrogen bonds       : angle       4.75844 /  3.37 ( 2115)
  metal coordination   : bond        0.00185 /  0.11 (    5)

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

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

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 174
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 LYS cc_start: 0.8503 (tptp) cc_final: 0.7795 (mtmt)
REVERT: B  233 TYR cc_start: 0.8165 (t80) cc_final: 0.7767 (t80)
REVERT: B  257 ILE cc_start: 0.7517 (tp) cc_final: 0.7239 (pt)
REVERT: C   41 ASP cc_start: 0.8090 (t70) cc_final: 0.7611 (t70)
REVERT: C  189 ILE cc_start: 0.8642 (mm) cc_final: 0.8362 (tt)
REVERT: D   28 GLU cc_start: 0.8535 (pt0) cc_final: 0.8282 (pt0)
REVERT: E  183 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.7858 (tp)
REVERT: E  750 MET cc_start: 0.8137 (tpp) cc_final: 0.7859 (tpp)
  outliers start: 33
  outliers final: 23
  residues processed: 195
  average time/residue: 0.1098
  time to fit residues: 32.6215
Evaluate side-chains
  188 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 164
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain B residue  113 ASP
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain D residue   67 SER
Chi-restraints excluded: chain E residue  122 SER
Chi-restraints excluded: chain E residue  128 LEU
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain E residue  257 LEU
Chi-restraints excluded: chain E residue  486 LEU
Chi-restraints excluded: chain E residue  488 THR
Chi-restraints excluded: chain E residue  503 LEU
Chi-restraints excluded: chain E residue  525 CYS
Chi-restraints excluded: chain E residue  551 HIS
Chi-restraints excluded: chain E residue  555 LEU
Chi-restraints excluded: chain E residue  642 VAL
Chi-restraints excluded: chain E residue  689 LEU
Chi-restraints excluded: chain E residue  745 VAL
Chi-restraints excluded: chain E residue  776 GLU
Chi-restraints excluded: chain F residue  123 CYS
Chi-restraints excluded: chain F residue  346 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   chunk 91 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 116 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 100 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 83 optimal weight:    0.0270
   overall best weight:    0.9242

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E 551 HIS ** 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 = 0.4074 r_free = 0.4074 target = 0.136160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.109743 restraints weight = 34966.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 2.48
r_work: 0.3508 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.2478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  16757  Z= 0.127
  Angle     :  0.580  12.006  23077  Z= 0.293
  Chirality :  0.043   0.300   2714
  Planarity :  0.004   0.054   2693
  Dihedral  : 17.233 177.282   3315
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 15.87 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.40 %
    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:  0.99 (0.20), residues: 1888
  helix:  1.82 (0.18), residues: 805
  sheet: -0.09 (0.28), residues: 341
  loop : -0.19 (0.24), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E  82 
 TYR   0.025   0.002   TYR D 101 
 PHE   0.023   0.001   PHE B 114 
 TRP   0.007   0.001   TRP E 115 
 HIS   0.003   0.001   HIS F 381 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.13 (16752)
  covalent geometry    : angle       0.58035 /  0.29 (23077)
  hydrogen bonds       : bond        0.03823 /  2.60 (  754)
  hydrogen bonds       : angle       4.76593 /  3.38 ( 2115)
  metal coordination   : bond        0.00158 /  0.10 (    5)

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

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

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 178
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 PRO cc_start: 0.8401 (Cg_exo) cc_final: 0.8162 (Cg_endo)
REVERT: B  233 TYR cc_start: 0.8180 (t80) cc_final: 0.7801 (t80)
REVERT: B  257 ILE cc_start: 0.7619 (tp) cc_final: 0.7361 (pt)
REVERT: C   41 ASP cc_start: 0.8096 (t70) cc_final: 0.7609 (t70)
REVERT: C  160 GLU cc_start: 0.7528 (pt0) cc_final: 0.7243 (pt0)
REVERT: C  189 ILE cc_start: 0.8651 (mm) cc_final: 0.8368 (tt)
REVERT: C  242 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7937 (mt-10)
REVERT: D   28 GLU cc_start: 0.8538 (pt0) cc_final: 0.8284 (pt0)
REVERT: D   84 ARG cc_start: 0.7182 (ptm160) cc_final: 0.6977 (ptp-110)
REVERT: E  183 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.7843 (tp)
REVERT: E  301 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7050 (p0)
REVERT: E  750 MET cc_start: 0.8074 (tpp) cc_final: 0.7835 (tpp)
REVERT: F  184 ASP cc_start: 0.7680 (t0) cc_final: 0.7053 (t70)
REVERT: F  188 ASP cc_start: 0.7885 (m-30) cc_final: 0.7272 (m-30)
  outliers start: 33
  outliers final: 22
  residues processed: 201
  average time/residue: 0.1162
  time to fit residues: 35.6025
Evaluate side-chains
  195 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 171
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain D residue   67 SER
Chi-restraints excluded: chain E residue  122 SER
Chi-restraints excluded: chain E residue  128 LEU
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain E residue  257 LEU
Chi-restraints excluded: chain E residue  301 ASP
Chi-restraints excluded: chain E residue  486 LEU
Chi-restraints excluded: chain E residue  488 THR
Chi-restraints excluded: chain E residue  503 LEU
Chi-restraints excluded: chain E residue  525 CYS
Chi-restraints excluded: chain E residue  551 HIS
Chi-restraints excluded: chain E residue  555 LEU
Chi-restraints excluded: chain E residue  628 LEU
Chi-restraints excluded: chain E residue  642 VAL
Chi-restraints excluded: chain E residue  689 LEU
Chi-restraints excluded: chain E residue  745 VAL
Chi-restraints excluded: chain E residue  776 GLU
Chi-restraints excluded: chain F residue  123 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 127 optimal weight:    6.9990
   chunk 166 optimal weight:    0.2980
   chunk 132 optimal weight:    8.9990
   chunk 123 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 178 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0870
   chunk 135 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.5158

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E 551 HIS ** 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 = 0.4087 r_free = 0.4087 target = 0.137077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.109830 restraints weight = 34845.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 2.59
r_work: 0.3522 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  16757  Z= 0.107
  Angle     :  0.573  12.214  23077  Z= 0.289
  Chirality :  0.042   0.303   2714
  Planarity :  0.004   0.050   2693
  Dihedral  : 17.178 175.043   3313
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 16.39 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.40 %
    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:  1.04 (0.20), residues: 1888
  helix:  1.88 (0.18), residues: 802
  sheet: -0.05 (0.28), residues: 336
  loop : -0.18 (0.24), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  82 
 TYR   0.022   0.001   TYR D 101 
 PHE   0.024   0.001   PHE B 114 
 TRP   0.007   0.001   TRP E 115 
 HIS   0.003   0.001   HIS E 601 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00233 /  0.11 (16752)
  covalent geometry    : angle       0.57326 /  0.29 (23077)
  hydrogen bonds       : bond        0.03639 /  2.48 (  754)
  hydrogen bonds       : angle       4.71064 /  3.33 ( 2115)
  metal coordination   : bond        0.00068 /  0.05 (    5)

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

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

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 178
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 PRO cc_start: 0.8269 (Cg_exo) cc_final: 0.8009 (Cg_endo)
REVERT: B   52 LYS cc_start: 0.8485 (tptp) cc_final: 0.7787 (mtmt)
REVERT: B  257 ILE cc_start: 0.7592 (tp) cc_final: 0.7240 (pt)
REVERT: C   41 ASP cc_start: 0.8081 (t70) cc_final: 0.7612 (t70)
REVERT: C  160 GLU cc_start: 0.7544 (pt0) cc_final: 0.7268 (pt0)
REVERT: C  189 ILE cc_start: 0.8630 (mm) cc_final: 0.8346 (tt)
REVERT: C  242 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7939 (mt-10)
REVERT: E  183 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.7882 (tp)
REVERT: E  486 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8040 (mp)
  outliers start: 26
  outliers final: 20
  residues processed: 195
  average time/residue: 0.1175
  time to fit residues: 34.5486
Evaluate side-chains
  190 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 168
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain B residue  113 ASP
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain D residue   67 SER
Chi-restraints excluded: chain E residue  122 SER
Chi-restraints excluded: chain E residue  128 LEU
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain E residue  257 LEU
Chi-restraints excluded: chain E residue  432 GLU
Chi-restraints excluded: chain E residue  486 LEU
Chi-restraints excluded: chain E residue  488 THR
Chi-restraints excluded: chain E residue  525 CYS
Chi-restraints excluded: chain E residue  551 HIS
Chi-restraints excluded: chain E residue  555 LEU
Chi-restraints excluded: chain E residue  642 VAL
Chi-restraints excluded: chain E residue  689 LEU
Chi-restraints excluded: chain E residue  745 VAL
Chi-restraints excluded: chain E residue  776 GLU
Chi-restraints excluded: chain F residue  123 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks:
   chunk 176 optimal weight:    5.9990
   chunk 188 optimal weight:    0.8980
   chunk 192 optimal weight:   10.0000
   chunk 8 optimal weight:    7.9990
   chunk 109 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0060
   chunk 4 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 96 optimal weight:    0.5980
   chunk 73 optimal weight:    8.9990
   overall best weight:    1.2998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 724 HIS ** 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 = 0.4061 r_free = 0.4061 target = 0.135299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.107852 restraints weight = 35008.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 2.52
r_work: 0.3486 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  16757  Z= 0.155
  Angle     :  0.619  13.099  23077  Z= 0.313
  Chirality :  0.043   0.299   2714
  Planarity :  0.004   0.056   2693
  Dihedral  : 17.172 173.420   3313
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 16.77 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.40 %
    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:  0.88 (0.20), residues: 1888
  helix:  1.74 (0.18), residues: 803
  sheet: -0.18 (0.28), residues: 338
  loop : -0.23 (0.24), residues: 747

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  82 
 TYR   0.037   0.002   TYR D 101 
 PHE   0.019   0.001   PHE B 114 
 TRP   0.007   0.001   TRP E 115 
 HIS   0.005   0.001   HIS E 749 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.15 (16752)
  covalent geometry    : angle       0.61857 /  0.31 (23077)
  hydrogen bonds       : bond        0.03920 /  2.67 (  754)
  hydrogen bonds       : angle       4.87584 /  3.47 ( 2115)
  metal coordination   : bond        0.00242 /  0.16 (    5)

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

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

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 169
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
REVERT: A  204 PRO cc_start: 0.8271 (Cg_exo) cc_final: 0.8016 (Cg_endo)
REVERT: B   52 LYS cc_start: 0.8503 (tptp) cc_final: 0.7802 (mtmt)
REVERT: B  233 TYR cc_start: 0.8150 (t80) cc_final: 0.7857 (t80)
REVERT: B  257 ILE cc_start: 0.7687 (tp) cc_final: 0.7322 (pt)
REVERT: C   41 ASP cc_start: 0.8069 (t70) cc_final: 0.7721 (t70)
REVERT: C  160 GLU cc_start: 0.7650 (pt0) cc_final: 0.7404 (pt0)
REVERT: C  189 ILE cc_start: 0.8681 (mm) cc_final: 0.8387 (tt)
REVERT: C  242 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8074 (mt-10)
REVERT: E  776 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8613 (pp20)
REVERT: F  184 ASP cc_start: 0.7685 (t0) cc_final: 0.7069 (t70)
REVERT: F  188 ASP cc_start: 0.7927 (m-30) cc_final: 0.7305 (m-30)
  outliers start: 24
  outliers final: 21
  residues processed: 183
  average time/residue: 0.1212
  time to fit residues: 33.7804
Evaluate side-chains
  186 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 164
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain D residue   67 SER
Chi-restraints excluded: chain E residue  122 SER
Chi-restraints excluded: chain E residue  128 LEU
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain E residue  257 LEU
Chi-restraints excluded: chain E residue  432 GLU
Chi-restraints excluded: chain E residue  486 LEU
Chi-restraints excluded: chain E residue  488 THR
Chi-restraints excluded: chain E residue  525 CYS
Chi-restraints excluded: chain E residue  551 HIS
Chi-restraints excluded: chain E residue  555 LEU
Chi-restraints excluded: chain E residue  642 VAL
Chi-restraints excluded: chain E residue  689 LEU
Chi-restraints excluded: chain E residue  720 ILE
Chi-restraints excluded: chain E residue  745 VAL
Chi-restraints excluded: chain E residue  776 GLU
Chi-restraints excluded: chain F residue  123 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 160 optimal weight:    4.9990
   chunk 148 optimal weight:    0.8980
   chunk 150 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 125 optimal weight:    0.0870
   chunk 142 optimal weight:    0.3980
   chunk 72 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 113 optimal weight:    0.0570
   overall best weight:    0.4076

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 724 HIS ** 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 = 0.4086 r_free = 0.4086 target = 0.137135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.109729 restraints weight = 34872.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 2.62
r_work: 0.3518 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.2755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  16757  Z= 0.107
  Angle     :  0.590  13.108  23077  Z= 0.297
  Chirality :  0.042   0.304   2714
  Planarity :  0.004   0.048   2693
  Dihedral  : 17.109 171.708   3313
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 17.03 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.40 %
    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:  0.95 (0.20), residues: 1888
  helix:  1.81 (0.19), residues: 802
  sheet: -0.12 (0.28), residues: 336
  loop : -0.22 (0.24), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  82 
 TYR   0.032   0.002   TYR D 101 
 PHE   0.023   0.001   PHE B 114 
 TRP   0.009   0.001   TRP E 357 
 HIS   0.003   0.001   HIS E 601 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00230 /  0.11 (16752)
  covalent geometry    : angle       0.58956 /  0.30 (23077)
  hydrogen bonds       : bond        0.03610 /  2.48 (  754)
  hydrogen bonds       : angle       4.75275 /  3.37 ( 2115)
  metal coordination   : bond        0.00053 /  0.03 (    5)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3219.69 seconds
wall clock time: 56 minutes 10.84 seconds (3370.84 seconds total)