Starting phenix.real_space_refine
on Fri Jul  3 04:55:07 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8a0e_15052/07_2026/8a0e_15052.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8a0e_15052/07_2026/8a0e_15052.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8a0e_15052/07_2026/8a0e_15052.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8a0e_15052/07_2026/8a0e_15052.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8a0e_15052/07_2026/8a0e_15052.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8a0e_15052/07_2026/8a0e_15052.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8a0e_15052/07_2026/8a0e_15052.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8a0e_15052/07_2026/8a0e_15052.cif"
  }
  resolution = 2.8
  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=   0.002 sd=   0.049
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: 5
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     S      70      5.16       5
     C    7638      2.51       5
     N    2069      2.21       5
     O    2297      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12082
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2770
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 356, 2767
          Classifications: {'peptide': 356}
          Link IDs: {'PTRANS': 16, 'TRANS': 339}
      Conformer: "B"
        Number of residues, atoms: 356, 2767
          Classifications: {'peptide': 356}
          Link IDs: {'PTRANS': 16, 'TRANS': 339}
          bond proxies already assigned to first conformer: 2820
    Chain: "B"
      Number of atoms: 2736
      Number of conformers: 2
      Conformer: "B"
        Number of residues, atoms: 352, 2733
          Classifications: {'peptide': 352}
          Link IDs: {'PTRANS': 16, 'TRANS': 335}
          Chain breaks: 1
      Conformer: "C"
        Number of residues, atoms: 352, 2733
          Classifications: {'peptide': 352}
          Link IDs: {'PTRANS': 16, 'TRANS': 335}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 2785
    Chain: "C"
      Number of atoms: 2724
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 350, 2720
          Classifications: {'peptide': 350}
          Link IDs: {'PTRANS': 15, 'TRANS': 334}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'CSS:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
      Conformer: "B"
        Number of residues, atoms: 350, 2720
          Classifications: {'peptide': 350}
          Link IDs: {'PTRANS': 15, 'TRANS': 334}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'CSS:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
          bond proxies already assigned to first conformer: 2771
    Chain: "D"
      Number of atoms: 2597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 332, 2597
          Classifications: {'peptide': 332}
          Link IDs: {'PTRANS': 13, 'TRANS': 318}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'CSS:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "E"
      Number of atoms: 1049
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 136, 1049
          Classifications: {'peptide': 136}
          Link IDs: {'PTRANS': 5, 'TRANS': 130}
    Chain: "A"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 54
          Unusual residues: {'NAD': 1, 'SPD': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 54
          Unusual residues: {'NAD': 1, 'SPD': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'NAD': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 54
          Unusual residues: {'NAD': 1, 'SPD': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 18
    residue:
      pdb=" N   ALA A  11 " occ=0.83
      ... (3 atoms not shown)
      pdb=" CB  ALA A  11 " occ=0.83
    residue:
      pdb=" N   LEU A  14 " occ=0.88
      ... (6 atoms not shown)
      pdb=" CD2 LEU A  14 " occ=0.88
    residue:
      pdb=" N   ALA A  15 " occ=0.94
      ... (3 atoms not shown)
      pdb=" CB  ALA A  15 " occ=0.94
    residue:
      pdb=" N   HIS A  20 " occ=0.95
      ... (8 atoms not shown)
      pdb=" NE2 HIS A  20 " occ=0.95
    residue:
      pdb=" N   PRO A  26 " occ=0.91
      ... (5 atoms not shown)
      pdb=" CD  PRO A  26 " occ=0.91
    residue:
      pdb=" N   ALA B  11 " occ=0.82
      ... (3 atoms not shown)
      pdb=" CB  ALA B  11 " occ=0.82
    residue:
      pdb=" N   LEU B  14 " occ=0.82
      ... (6 atoms not shown)
      pdb=" CD2 LEU B  14 " occ=0.82
    residue:
      pdb=" N   ALA B  15 " occ=0.90
      ... (3 atoms not shown)
      pdb=" CB  ALA B  15 " occ=0.90
    residue:
      pdb=" N   HIS B  20 " occ=0.91
      ... (8 atoms not shown)
      pdb=" NE2 HIS B  20 " occ=0.91
    residue:
      pdb=" N   ALA C  11 " occ=0.83
      ... (3 atoms not shown)
      pdb=" CB  ALA C  11 " occ=0.83
    residue:
      pdb=" N   LEU C  14 " occ=0.88
      ... (6 atoms not shown)
      pdb=" CD2 LEU C  14 " occ=0.88
    residue:
      pdb=" N   ALA C  15 " occ=0.94
      ... (3 atoms not shown)
      pdb=" CB  ALA C  15 " occ=0.94
    ... (remaining 6 not shown)
  Time building chain proxies: 4.27, per 1000 atoms: 0.35
  Number of scatterers: 12082
  At special positions: 0
  Unit cell: (92.02, 96.32, 149.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      70     16.00
     P       8     15.00
     O    2297      8.00
     N    2069      7.00
     C    7638      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  73 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.07
  Conformation dependent library (CDL) restraints added in 761.1 milliseconds
  

  3014 Ramachandran restraints generated.
    1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2820

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 12 sheets defined
      50.1% alpha, 10.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 18
      removed outlier: 3.693A  pdb=" N   ALA A  16 " --> pdb=" O   GLY A  12 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   VAL A  17 " --> pdb=" O   ALA A  13 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   LEU A  18 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 39
      removed outlier: 3.613A  pdb=" N   ARG A  38 " --> pdb=" O   ASP A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 48
    Processing helix  chain 'A' and resid 49 through 52
    Processing helix  chain 'A' and resid 55 through 74
    Processing helix  chain 'A' and resid 112 through 122
      removed outlier: 3.973A  pdb=" N   TYR A 118 " --> pdb=" O   GLU A 114 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU A 119 " --> pdb=" O   THR A 115 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   HIS A 122 " --> pdb=" O   TYR A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 142
      removed outlier: 3.848A  pdb=" N   VAL A 135 " --> pdb=" O   THR A 131 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ASP A 138 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   CYS A 142 " --> pdb=" O   ASP A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 161
    Processing helix  chain 'A' and resid 173 through 197
      removed outlier: 3.700A  pdb=" N   PHE A 179 " --> pdb=" O   ASN A 175 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLU A 180 " --> pdb=" O   TYR A 176 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ASP A 181 " --> pdb=" O   CYS A 177 " (cutoff:3.500A)
      Proline residue:  A 185  - end of helix
      removed outlier: 3.501A  pdb=" N   ASN A 195 " --> pdb=" O   VAL A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 215
      removed outlier: 3.773A  pdb=" N   LYS A 212 " --> pdb=" O   ALA A 208 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLU A 213 " --> pdb=" O   ARG A 209 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   ASN A 215 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 227
      removed outlier: 3.577A  pdb=" N   TRP A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 249
    Processing helix  chain 'A' and resid 259 through 272
      removed outlier: 3.790A  pdb=" N   LEU A 263 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ALA A 270 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 296
      removed outlier: 3.839A  pdb=" N   HIS A 288 " --> pdb=" O   GLY A 284 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   MET A 296 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 327
      removed outlier: 3.968A  pdb=" N   ALA A 324 " --> pdb=" O   ARG A 320 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   VAL A 325 " --> pdb=" O   PRO A 321 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   SER A 326 " --> pdb=" O   ASP A 322 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   TRP A 327 " --> pdb=" O   GLU A 323 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 320 through 327'
    Processing helix  chain 'A' and resid 342 through 354
      removed outlier: 3.504A  pdb=" N   VAL A 346 " --> pdb=" O   ASP A 342 " (cutoff:3.500A)
      Proline residue:  A 348  - end of helix
      removed outlier: 3.605A  pdb=" N   GLU A 353 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 363
    Processing helix  chain 'B' and resid 10 through 18
      removed outlier: 3.523A  pdb=" N   LEU B  14 " --> pdb=" O   PRO B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 39
      removed outlier: 3.957A  pdb=" N   ARG B  38 " --> pdb=" O   ASP B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 46
    Processing helix  chain 'B' and resid 47 through 52
      removed outlier: 3.572A  pdb=" N   GLY B  50 " --> pdb=" O   GLU B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 74
      removed outlier: 3.681A  pdb=" N   THR B  57 " --> pdb=" O   GLY B  53 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ASN B  58 " --> pdb=" O   PHE B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 122
      removed outlier: 3.781A  pdb=" N   TYR B 118 " --> pdb=" O   GLU B 114 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   HIS B 122 " --> pdb=" O   TYR B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 141
      removed outlier: 4.064A  pdb=" N   ASP B 138 " --> pdb=" O   GLY B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 161
      removed outlier: 3.654A  pdb=" N   ASN B 161 " --> pdb=" O   GLU B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 196
      removed outlier: 3.635A  pdb=" N   PHE B 179 " --> pdb=" O   ASN B 175 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLU B 180 " --> pdb=" O   TYR B 176 " (cutoff:3.500A)
      Proline residue:  B 185  - end of helix
      removed outlier: 3.551A  pdb=" N   MET B 192 " --> pdb=" O   ASP B 188 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLU B 193 " --> pdb=" O   GLN B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 215
      removed outlier: 3.903A  pdb=" N   ASN B 215 " --> pdb=" O   GLY B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 227
      removed outlier: 3.682A  pdb=" N   TRP B 223 " --> pdb=" O   SER B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 249
    Processing helix  chain 'B' and resid 259 through 272
      removed outlier: 3.648A  pdb=" N   LEU B 263 " --> pdb=" O   ILE B 259 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ALA B 270 " --> pdb=" O   ILE B 266 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ILE B 271 " --> pdb=" O   ASN B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 296
      removed outlier: 3.703A  pdb=" N   HIS B 288 " --> pdb=" O   GLY B 284 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   MET B 296 " --> pdb=" O   ASN B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 327
      removed outlier: 4.304A  pdb=" N   ALA B 324 " --> pdb=" O   ARG B 320 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   VAL B 325 " --> pdb=" O   PRO B 321 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER B 326 " --> pdb=" O   ASP B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 355
      removed outlier: 3.549A  pdb=" N   VAL B 346 " --> pdb=" O   ASP B 342 " (cutoff:3.500A)
      Proline residue:  B 348  - end of helix
      removed outlier: 3.551A  pdb=" N   GLU B 353 " --> pdb=" O   LEU B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 363
      removed outlier: 3.750A  pdb=" N   MET B 363 " --> pdb=" O   ASP B 360 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 11 through 18
    Processing helix  chain 'C' and resid 35 through 39
      removed outlier: 3.814A  pdb=" N   ARG C  38 " --> pdb=" O   ASP C  35 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 48
      removed outlier: 3.510A  pdb=" N   GLU C  47 " --> pdb=" O   ARG C  43 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 54 through 74
      removed outlier: 3.993A  pdb=" N   ASN C  58 " --> pdb=" O   PHE C  54 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 84 through 89
      removed outlier: 3.739A  pdb=" N   THR C  88 " --> pdb=" O   HIS C  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 122
      removed outlier: 3.511A  pdb=" N   ARG C 117 " --> pdb=" O   ARG C 113 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU C 119 " --> pdb=" O   THR C 115 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   HIS C 122 " --> pdb=" O   TYR C 118 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 131 through 141
      removed outlier: 3.553A  pdb=" N   VAL C 135 " --> pdb=" O   THR C 131 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ASP C 138 " --> pdb=" O   GLY C 134 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU C 139 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 154 through 161
      removed outlier: 3.619A  pdb=" N   LEU C 158 " --> pdb=" O   ARG C 154 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ASN C 161 " --> pdb=" O   GLU C 157 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 174 through 197
      removed outlier: 3.521A  pdb=" N   GLU C 180 " --> pdb=" O   TYR C 176 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ASP C 181 " --> pdb=" O   CSS C 177 " (cutoff:3.500A)
      Proline residue:  C 185  - end of helix
      removed outlier: 3.657A  pdb=" N   GLN C 189 " --> pdb=" O   PRO C 185 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 215
      removed outlier: 3.885A  pdb=" N   ASN C 215 " --> pdb=" O   GLY C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 219 through 227
      removed outlier: 3.733A  pdb=" N   TRP C 223 " --> pdb=" O   SER C 219 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 239 through 249
    Processing helix  chain 'C' and resid 259 through 272
      removed outlier: 3.587A  pdb=" N   PHE C 272 " --> pdb=" O   THR C 268 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 284 through 296
      removed outlier: 3.832A  pdb=" N   HIS C 288 " --> pdb=" O   GLY C 284 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   MET C 296 " --> pdb=" O   ASN C 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 320 through 327
      removed outlier: 3.865A  pdb=" N   ALA C 324 " --> pdb=" O   ARG C 320 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   VAL C 325 " --> pdb=" O   PRO C 321 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   SER C 326 " --> pdb=" O   ASP C 322 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   TRP C 327 " --> pdb=" O   GLU C 323 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 320 through 327'
    Processing helix  chain 'C' and resid 342 through 354
      removed outlier: 3.608A  pdb=" N   VAL C 346 " --> pdb=" O   ASP C 342 " (cutoff:3.500A)
      Proline residue:  C 348  - end of helix
    Processing helix  chain 'C' and resid 358 through 362
    Processing helix  chain 'D' and resid 35 through 39
      removed outlier: 3.518A  pdb=" N   ARG D  38 " --> pdb=" O   ASP D  35 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 41 through 48
    Processing helix  chain 'D' and resid 49 through 52
    Processing helix  chain 'D' and resid 53 through 74
      removed outlier: 3.711A  pdb=" N   THR D  57 " --> pdb=" O   GLY D  53 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ASN D  58 " --> pdb=" O   PHE D  54 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 84 through 89
    Processing helix  chain 'D' and resid 112 through 122
      removed outlier: 3.967A  pdb=" N   TYR D 118 " --> pdb=" O   GLU D 114 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   HIS D 122 " --> pdb=" O   TYR D 118 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 132 through 141
      removed outlier: 3.616A  pdb=" N   GLU D 137 " --> pdb=" O   GLY D 133 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   ASP D 138 " --> pdb=" O   GLY D 134 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 154 through 161
      removed outlier: 3.668A  pdb=" N   LEU D 158 " --> pdb=" O   ARG D 154 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 174 through 197
      removed outlier: 3.528A  pdb=" N   LYS D 178 " --> pdb=" O   GLU D 174 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   PHE D 179 " --> pdb=" O   ASN D 175 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLU D 180 " --> pdb=" O   TYR D 176 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ASP D 181 " --> pdb=" O   CSS D 177 " (cutoff:3.500A)
      Proline residue:  D 185  - end of helix
    Processing helix  chain 'D' and resid 202 through 215
      removed outlier: 4.093A  pdb=" N   ASN D 215 " --> pdb=" O   GLY D 211 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 219 through 227
      removed outlier: 3.687A  pdb=" N   TRP D 223 " --> pdb=" O   SER D 219 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 239 through 249
      removed outlier: 3.508A  pdb=" N   ASP D 243 " --> pdb=" O   GLY D 239 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 259 through 272
      removed outlier: 3.696A  pdb=" N   ARG D 264 " --> pdb=" O   VAL D 260 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   LEU D 265 " --> pdb=" O   GLU D 261 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE D 266 " --> pdb=" O   ASP D 262 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ALA D 270 " --> pdb=" O   ILE D 266 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 284 through 296
      removed outlier: 3.652A  pdb=" N   HIS D 288 " --> pdb=" O   GLY D 284 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   MET D 296 " --> pdb=" O   ASN D 292 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 320 through 327
      removed outlier: 4.037A  pdb=" N   ALA D 324 " --> pdb=" O   ARG D 320 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL D 325 " --> pdb=" O   PRO D 321 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   SER D 326 " --> pdb=" O   ASP D 322 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   TRP D 327 " --> pdb=" O   GLU D 323 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 320 through 327'
    Processing helix  chain 'D' and resid 342 through 355
      Proline residue:  D 348  - end of helix
    Processing helix  chain 'D' and resid 356 through 363
      removed outlier: 3.873A  pdb=" N   MET D 359 " --> pdb=" O   ALA D 356 " (cutoff:3.500A)
      removed outlier: 5.614A  pdb=" N   ASP D 360 " --> pdb=" O   GLN D 357 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA D 361 " --> pdb=" O   LYS D 358 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 128
      removed outlier: 4.207A  pdb=" N   GLU E 124 " --> pdb=" O   GLY E 120 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   LYS E 126 " --> pdb=" O   GLU E 122 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   TYR E 127 " --> pdb=" O   ILE E 123 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   ASP E 128 " --> pdb=" O   GLU E 124 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 231 through 232
      removed outlier: 6.821A  pdb=" N   LEU A 128 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   THR A  98 " --> pdb=" O   GLY A 277 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   ILE A 279 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   PHE A 100 " --> pdb=" O   ILE A 279 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   LEU A 281 " --> pdb=" O   PHE A 100 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   GLY A 102 " --> pdb=" O   LEU A 281 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   TYR A 302 " --> pdb=" O   THR A 276 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 148
      removed outlier: 3.524A  pdb=" N   TYR A 147 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 231 through 232
      removed outlier: 6.744A  pdb=" N   LEU B 128 " --> pdb=" O   PHE B 232 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   THR B  98 " --> pdb=" O   GLY B 277 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   ILE B 279 " --> pdb=" O   THR B  98 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   PHE B 100 " --> pdb=" O   ILE B 279 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   LEU B 281 " --> pdb=" O   PHE B 100 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   GLY B 102 " --> pdb=" O   LEU B 281 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   TYR B 302 " --> pdb=" O   THR B 276 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 147 through 148
    Processing sheet with id=AA5, first strand: chain 'C' and resid 231 through 232
      removed outlier: 6.897A  pdb=" N   LEU C 128 " --> pdb=" O   PHE C 232 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   TYR C 302 " --> pdb=" O   THR C 276 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 147 through 148
    Processing sheet with id=AA7, first strand: chain 'D' and resid 231 through 232
      removed outlier: 6.831A  pdb=" N   LEU D 128 " --> pdb=" O   PHE D 232 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TYR D 302 " --> pdb=" O   THR D 276 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   ALA D 303 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 8.261A  pdb=" N   VAL D 339 " --> pdb=" O   ALA D 303 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   TYR D 305 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 147 through 148
    Processing sheet with id=AA9, first strand: chain 'E' and resid 17 through 21
    Processing sheet with id=AB1, first strand: chain 'E' and resid 30 through 32
      removed outlier: 6.811A  pdb=" N   VAL E  59 " --> pdb=" O   VAL E  41 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   MET E  43 " --> pdb=" O   HIS E  57 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   HIS E  57 " --> pdb=" O   MET E  43 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   THR E  45 " --> pdb=" O   LYS E  55 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   LYS E  55 " --> pdb=" O   THR E  45 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 85 through 88
      removed outlier: 3.572A  pdb=" N   ASN E  87 " --> pdb=" O   VAL E 137 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU E 138 " --> pdb=" O   ALA E 145 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ALA E 145 " --> pdb=" O   LEU E 138 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 85 through 88
      removed outlier: 3.572A  pdb=" N   ASN E  87 " --> pdb=" O   VAL E 137 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LYS E 150 " --> pdb=" O   LEU E 134 " (cutoff:3.500A)

    462 hydrogen bonds defined for protein.
    1290 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.17

  Time building geometry restraints manager: 1.37 seconds

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

  Histogram of bond lengths:
        1.23 -     1.40: 4991
        1.40 -     1.58: 7209
        1.58 -     1.75: 16
        1.75 -     1.93: 116
        1.93 -     2.11: 2
  Bond restraints: 12334
  Sorted by residual:
  bond pdb=" CB  CSS D 177 "
       pdb=" SG  CSS D 177 "
    ideal  model  delta    sigma   weight residual
    1.823  1.755  0.068 2.00e-02 2.50e+03 1.15e+01
  bond pdb=" CB  CSS C 177 "
       pdb=" SG  CSS C 177 "
    ideal  model  delta    sigma   weight residual
    1.823  1.756  0.067 2.00e-02 2.50e+03 1.11e+01
  bond pdb=" O3  NAD D 402 "
       pdb=" PA  NAD D 402 "
    ideal  model  delta    sigma   weight residual
    1.653  1.603  0.050 2.00e-02 2.50e+03 6.31e+00
  bond pdb=" O3  NAD A 401 "
       pdb=" PA  NAD A 401 "
    ideal  model  delta    sigma   weight residual
    1.653  1.603  0.050 2.00e-02 2.50e+03 6.18e+00
  bond pdb=" O3  NAD C 401 "
       pdb=" PA  NAD C 401 "
    ideal  model  delta    sigma   weight residual
    1.653  1.604  0.049 2.00e-02 2.50e+03 6.11e+00
  ... (remaining 12329 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.73: 16597
        2.73 -     5.47: 135
        5.47 -     8.20: 6
        8.20 -    10.94: 2
       10.94 -    13.67: 1
  Bond angle restraints: 16741
  Sorted by residual:
  angle pdb=" CA  CYS A 177 "
        pdb=" C   CYS A 177 "
        pdb=" O   CYS A 177 "
      ideal   model   delta    sigma   weight residual
     119.60  123.92   -4.32 1.17e+00 7.31e-01 1.36e+01
  angle pdb=" PA  NAD A 401 "
        pdb=" O3  NAD A 401 "
        pdb=" PN  NAD A 401 "
      ideal   model   delta    sigma   weight residual
     126.50  136.85  -10.35 3.00e+00 1.11e-01 1.19e+01
  angle pdb=" N   CYS A 177 "
        pdb=" CA  CYS A 177 "
        pdb=" C   CYS A 177 "
      ideal   model   delta    sigma   weight residual
     112.90  108.56    4.34 1.31e+00 5.83e-01 1.10e+01
  angle pdb=" PA  NAD B 401 "
        pdb=" O3  NAD B 401 "
        pdb=" PN  NAD B 401 "
      ideal   model   delta    sigma   weight residual
     126.50  134.95   -8.45 3.00e+00 1.11e-01 7.93e+00
  angle pdb=" PA  NAD C 401 "
        pdb=" O3  NAD C 401 "
        pdb=" PN  NAD C 401 "
      ideal   model   delta    sigma   weight residual
     126.50  134.07   -7.57 3.00e+00 1.11e-01 6.37e+00
  ... (remaining 16736 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 6787
       18.00 -    35.99: 414
       35.99 -    53.99: 82
       53.99 -    71.99: 18
       71.99 -    89.99: 13
  Dihedral angle restraints: 7314
    sinusoidal: 2919
      harmonic: 4395
  Sorted by residual:
  dihedral pdb=" CA  CYS E  73 "
           pdb=" C   CYS E  73 "
           pdb=" N   PRO E  74 "
           pdb=" CA  PRO E  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.50   32.50     0      5.00e+00 4.00e-02 4.23e+01
  dihedral pdb=" CB  CYS E  22 "
           pdb=" SG  CYS E  22 "
           pdb=" SG  CYS E  73 "
           pdb=" CB  CYS E  73 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -136.15   50.15     1      1.00e+01 1.00e-02 3.45e+01
  dihedral pdb=" CA  GLY A  53 "
           pdb=" C   GLY A  53 "
           pdb=" N   PHE A  54 "
           pdb=" CA  PHE A  54 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.17  -19.83     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 7311 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1447
       0.047 -    0.095: 323
       0.095 -    0.142: 105
       0.142 -    0.190: 1
       0.190 -    0.237: 5
  Chirality restraints: 1881
  Sorted by residual:
  chirality pdb=" C1D NAD C 401 "
            pdb=" C2D NAD C 401 "
            pdb=" N1N NAD C 401 "
            pdb=" O4D NAD C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.41    2.65   -0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" C1D NAD A 401 "
            pdb=" C2D NAD A 401 "
            pdb=" N1N NAD A 401 "
            pdb=" O4D NAD A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.41    2.65   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" C1D NAD B 401 "
            pdb=" C2D NAD B 401 "
            pdb=" N1N NAD B 401 "
            pdb=" O4D NAD B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.41    2.64   -0.23 2.00e-01 2.50e+01 1.28e+00
  ... (remaining 1878 not shown)

  Planarity restraints: 2151
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1D NAD D 402 "    0.034 2.00e-02 2.50e+03   2.43e-02 1.18e+01
        pdb=" C2N NAD D 402 "   -0.052 2.00e-02 2.50e+03
        pdb=" C3N NAD D 402 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4N NAD D 402 "    0.012 2.00e-02 2.50e+03
        pdb=" C5N NAD D 402 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6N NAD D 402 "   -0.004 2.00e-02 2.50e+03
        pdb=" C7N NAD D 402 "    0.024 2.00e-02 2.50e+03
        pdb=" N1N NAD D 402 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E  36 "   -0.033 5.00e-02 4.00e+02   5.07e-02 4.11e+00
        pdb=" N   PRO E  37 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO E  37 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO E  37 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 202 "    0.028 5.00e-02 4.00e+02   4.17e-02 2.78e+00
        pdb=" N   PRO C 203 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO C 203 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C 203 "    0.023 5.00e-02 4.00e+02
  ... (remaining 2148 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 374
        2.72 -     3.27: 11459
        3.27 -     3.81: 18027
        3.81 -     4.36: 24580
        4.36 -     4.90: 41298
  Nonbonded interactions: 95738
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 105 "
            pdb=" OG1 THR C 131 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" OG  SER A 315 "
            pdb=" O1A NAD B 401 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OG  SER A 105 "
            pdb=" OG1 THR A 131 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   GLU A 323 "
            pdb=" OG  SER A 326 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OG  SER D 105 "
            pdb=" OG1 THR D 131 "
     model   vdw
     2.245 3.040
  ... (remaining 95733 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 28 through 79 or resid 84 through 104 or resid 106 through \ 
 176 or resid 178 through 239 or resid 241 through 285 or resid 287 through 363) \ 
)
  selection = (chain 'B' and (resid 28 through 104 or resid 106 through 176 or resid 178 throu \ 
gh 239 or resid 241 through 285 or resid 287 through 363))
  selection = (chain 'C' and (resid 28 through 104 or resid 106 through 176 or resid 178 throu \ 
gh 239 or resid 241 through 285 or resid 287 through 363))
  selection = (chain 'D' and (resid 28 through 104 or resid 106 through 176 or resid 178 throu \ 
gh 239 or resid 241 through 285 or resid 287 through 363))
}

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=0.21 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.220
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8904
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      :  0.003   0.068  12335  Z= 0.168
  Angle     :  0.598  13.671  16743  Z= 0.298
  Chirality :  0.044   0.237   1881
  Planarity :  0.004   0.051   2151
  Dihedral  : 13.096  89.986   4491
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.54 %
    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: -0.22 (0.22), residues: 1507
  helix: -0.14 (0.21), residues: 611
  sheet:  2.00 (0.40), residues: 185
  loop : -0.66 (0.22), residues: 711

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 331 
 TYR   0.013   0.001   TYR B 221 
 PHE   0.014   0.001   PHE C 355 
 TRP   0.018   0.001   TRP B 327 
 HIS   0.008   0.001   HIS B 289 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.17 (12334)
  covalent geometry    : angle       0.59752 /  0.30 (16741)
  SS BOND              : bond        0.00584 /  0.31 (    1)
  SS BOND              : angle       1.90397 /  1.12 (    2)
  hydrogen bonds       : bond        0.22708 / 14.75 (  459)
  hydrogen bonds       : angle       6.85438 /  5.02 ( 1290)

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

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

  3014 Ramachandran restraints generated.
    1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3014 Ramachandran restraints generated.
    1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.489 
Fit side-chains
REVERT: A  359 MET cc_start: 0.7538 (tpt) cc_final: 0.7328 (tpt)
REVERT: B  251 LYS cc_start: 0.7882 (mmtm) cc_final: 0.7679 (mptt)
REVERT: B  252 ASN cc_start: 0.8136 (m-40) cc_final: 0.7888 (m-40)
REVERT: C   86 ASP cc_start: 0.7987 (m-30) cc_final: 0.7344 (p0)
REVERT: E  141 MET cc_start: 0.4947 (ptm) cc_final: 0.4626 (pmt)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.7526
  time to fit residues: 117.3708
Evaluate side-chains
  114 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    0.3980
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.0470
   chunk 149 optimal weight:   20.0000
   overall best weight:    1.8882

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 173 ASN
B 298 ASN
D 252 ASN
E  57 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.126260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.091739 restraints weight = 30604.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 2.57
r_work: 0.2903 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2781 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2781
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2781 r_free = 0.2781    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2779 r_free = 0.2779    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 18 (31 function evaluations)
r_final: 0.2779
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9072
moved from start:          0.1019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12335  Z= 0.143
  Angle     :  0.549  13.276  16743  Z= 0.284
  Chirality :  0.043   0.160   1881
  Planarity :  0.004   0.046   2151
  Dihedral  :  6.554  59.896   1685
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  6.02 %
    Favored  : 93.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.21), residues: 1507
  helix:  0.26 (0.21), residues: 634
  sheet:  2.00 (0.41), residues: 179
  loop : -0.67 (0.22), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 331 
 TYR   0.015   0.001   TYR C 221 
 PHE   0.018   0.001   PHE C 355 
 TRP   0.017   0.001   TRP B 327 
 HIS   0.007   0.001   HIS B 289 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.14 (12334)
  covalent geometry    : angle       0.54871 /  0.28 (16741)
  SS BOND              : bond        0.00362 /  0.19 (    1)
  SS BOND              : angle       1.31694 /  0.75 (    2)
  hydrogen bonds       : bond        0.06118 /  4.16 (  459)
  hydrogen bonds       : angle       4.80954 /  3.48 ( 1290)

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

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

  3014 Ramachandran restraints generated.
    1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3014 Ramachandran restraints generated.
    1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 130
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6256 (mp)
REVERT: B  157 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7285 (mp0)
REVERT: B  251 LYS cc_start: 0.8147 (mmtm) cc_final: 0.7900 (mptt)
REVERT: B  252 ASN cc_start: 0.8551 (m-40) cc_final: 0.8292 (m110)
REVERT: C   86 ASP cc_start: 0.8001 (m-30) cc_final: 0.7703 (m-30)
REVERT: C  359 MET cc_start: 0.8113 (tpt) cc_final: 0.7857 (tpt)
REVERT: C  363 MET cc_start: 0.6479 (OUTLIER) cc_final: 0.5936 (mpm)
REVERT: D  189 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7259 (mm-40)
REVERT: D  251 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8570 (mtmt)
REVERT: E  141 MET cc_start: 0.5028 (ptm) cc_final: 0.4657 (pmt)
  outliers start: 9
  outliers final: 2
  residues processed: 132
  average time/residue: 0.7053
  time to fit residues: 98.9650
Evaluate side-chains
  129 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 123
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain C residue  363 MET
Chi-restraints excluded: chain D residue  251 LYS
Chi-restraints excluded: chain E residue   75 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 147 optimal weight:    8.9990
   chunk 17 optimal weight:    0.9980
   chunk 150 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 101 optimal weight:    8.9990
   chunk 74 optimal weight:    5.9990
   chunk 95 optimal weight:    7.9990
   chunk 103 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   overall best weight:    2.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 122 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.123283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.088827 restraints weight = 32359.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 2.82
r_work: 0.2849 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2723 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2718
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 10 (18 function evaluations)
r_final: 0.2718
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9112
moved from start:          0.1369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  12335  Z= 0.198
  Angle     :  0.599  12.093  16743  Z= 0.312
  Chirality :  0.046   0.174   1881
  Planarity :  0.005   0.050   2151
  Dihedral  :  6.646  63.248   1685
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 1.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  6.10 %
    Favored  : 92.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.54 %
    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: -0.09 (0.21), residues: 1507
  helix:  0.30 (0.21), residues: 641
  sheet:  1.89 (0.40), residues: 179
  loop : -0.91 (0.21), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  91 
 TYR   0.019   0.002   TYR C 221 
 PHE   0.023   0.002   PHE C 355 
 TRP   0.019   0.001   TRP B 327 
 HIS   0.010   0.002   HIS D 289 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00480 /  0.20 (12334)
  covalent geometry    : angle       0.59855 /  0.31 (16741)
  SS BOND              : bond        0.00330 /  0.17 (    1)
  SS BOND              : angle       1.99477 /  1.16 (    2)
  hydrogen bonds       : bond        0.06994 /  4.78 (  459)
  hydrogen bonds       : angle       4.63561 /  3.33 ( 1290)

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

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

  3014 Ramachandran restraints generated.
    1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3014 Ramachandran restraints generated.
    1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A   18 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.6311 (mp)
REVERT: A  114 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7801 (mm-30)
REVERT: B  157 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7349 (mp0)
REVERT: C   71 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8073 (mp0)
REVERT: C   86 ASP cc_start: 0.7993 (m-30) cc_final: 0.7734 (m-30)
REVERT: C  189 GLN cc_start: 0.8318 (mt0) cc_final: 0.8104 (mm110)
REVERT: C  359 MET cc_start: 0.8138 (tpt) cc_final: 0.7920 (tpt)
REVERT: C  363 MET cc_start: 0.6295 (OUTLIER) cc_final: 0.5843 (mpm)
REVERT: D  251 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8571 (mtmt)
  outliers start: 21
  outliers final: 8
  residues processed: 129
  average time/residue: 0.7308
  time to fit residues: 100.2732
Evaluate side-chains
  133 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain C residue   71 GLU
Chi-restraints excluded: chain C residue  363 MET
Chi-restraints excluded: chain D residue  196 THR
Chi-restraints excluded: chain D residue  251 LYS
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain D residue  363 MET
Chi-restraints excluded: chain E residue   75 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 124 optimal weight:    0.9980
   chunk 147 optimal weight:    6.9990
   chunk 41 optimal weight:    4.9990
   chunk 89 optimal weight:    5.9990
   chunk 63 optimal weight:   10.0000
   chunk 34 optimal weight:    0.7980
   chunk 120 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0070
   chunk 134 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 106 optimal weight:    5.9990
   overall best weight:    1.7602

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  83 GLN
B 252 ASN
C 298 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.125160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.090941 restraints weight = 35259.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 2.92
r_work: 0.2872 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2865
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2865 r_free = 0.2865    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (19 function evaluations)
r_final: 0.2866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8998
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12335  Z= 0.131
  Angle     :  0.523  12.013  16743  Z= 0.271
  Chirality :  0.043   0.157   1881
  Planarity :  0.004   0.050   2151
  Dihedral  :  6.460  64.046   1685
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 2.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  7.82 %
    Favored  : 91.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.54 %
    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:  0.05 (0.21), residues: 1507
  helix:  0.50 (0.21), residues: 641
  sheet:  1.90 (0.40), residues: 174
  loop : -0.87 (0.21), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  91 
 TYR   0.014   0.001   TYR C 221 
 PHE   0.016   0.001   PHE C 355 
 TRP   0.019   0.001   TRP B 327 
 HIS   0.006   0.001   HIS B 289 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.13 (12334)
  covalent geometry    : angle       0.52236 /  0.27 (16741)
  SS BOND              : bond        0.00530 /  0.28 (    1)
  SS BOND              : angle       1.63825 /  0.95 (    2)
  hydrogen bonds       : bond        0.05283 /  3.61 (  459)
  hydrogen bonds       : angle       4.33103 /  3.12 ( 1290)

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

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

  3014 Ramachandran restraints generated.
    1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3014 Ramachandran restraints generated.
    1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 123
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A   32 ARG cc_start: 0.8269 (tpp-160) cc_final: 0.8005 (ttm110)
REVERT: A  114 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7502 (mm-30)
REVERT: C   86 ASP cc_start: 0.7970 (m-30) cc_final: 0.7716 (m-30)
REVERT: C  189 GLN cc_start: 0.8139 (mt0) cc_final: 0.7914 (mm110)
REVERT: C  363 MET cc_start: 0.6232 (OUTLIER) cc_final: 0.5838 (mpm)
  outliers start: 14
  outliers final: 7
  residues processed: 130
  average time/residue: 0.7578
  time to fit residues: 104.8280
Evaluate side-chains
  127 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue  363 MET
Chi-restraints excluded: chain D residue   89 GLN
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain E residue   75 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 109 optimal weight:    0.6980
   chunk 88 optimal weight:    0.0970
   chunk 114 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   chunk 81 optimal weight:    8.9990
   chunk 23 optimal weight:    5.9990
   chunk 22 optimal weight:    0.0270
   chunk 125 optimal weight:    0.9980
   chunk 133 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   overall best weight:    0.5638

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 252 ASN
B 292 ASN
C 298 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.129403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.097298 restraints weight = 24417.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 2.37
r_work: 0.2978 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2855 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2842
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2842 r_free = 0.2842    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 8 (16 function evaluations)
r_final: 0.2841
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8996
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  12335  Z= 0.082
  Angle     :  0.447  10.658  16743  Z= 0.229
  Chirality :  0.040   0.141   1881
  Planarity :  0.004   0.048   2151
  Dihedral  :  6.024  60.295   1685
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 2.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  8.37 %
    Favored  : 90.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.21), residues: 1507
  helix:  0.81 (0.21), residues: 639
  sheet:  1.91 (0.40), residues: 177
  loop : -0.74 (0.22), residues: 691

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  91 
 TYR   0.008   0.001   TYR C 221 
 PHE   0.007   0.001   PHE C 355 
 TRP   0.019   0.001   TRP B 327 
 HIS   0.004   0.001   HIS B 289 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00169 /  0.08 (12334)
  covalent geometry    : angle       0.44633 /  0.23 (16741)
  SS BOND              : bond        0.00682 /  0.36 (    1)
  SS BOND              : angle       1.30226 /  0.75 (    2)
  hydrogen bonds       : bond        0.03388 /  2.31 (  459)
  hydrogen bonds       : angle       3.89241 /  2.83 ( 1290)

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

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

  3014 Ramachandran restraints generated.
    1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3014 Ramachandran restraints generated.
    1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 126
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A   32 ARG cc_start: 0.8353 (tpp-160) cc_final: 0.8114 (ttm110)
REVERT: A  150 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7872 (mp0)
REVERT: C   86 ASP cc_start: 0.7946 (m-30) cc_final: 0.7682 (m-30)
REVERT: C  189 GLN cc_start: 0.8255 (mt0) cc_final: 0.8037 (mm110)
  outliers start: 13
  outliers final: 5
  residues processed: 132
  average time/residue: 0.6896
  time to fit residues: 96.9811
Evaluate side-chains
  123 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  240 SER
Chi-restraints excluded: chain E residue   75 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 111 optimal weight:    0.0030
   chunk 38 optimal weight:    5.9990
   chunk 127 optimal weight:    8.9990
   chunk 37 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 112 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 118 optimal weight:    8.9990
   chunk 67 optimal weight:    7.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    1.7794

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 292 ASN
E  77 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.125937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.092498 restraints weight = 22989.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 2.23
r_work: 0.2912 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2793 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2784
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 7 (14 function evaluations)
r_final: 0.2784
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9055
moved from start:          0.1565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12335  Z= 0.129
  Angle     :  0.508   9.077  16743  Z= 0.264
  Chirality :  0.042   0.159   1881
  Planarity :  0.004   0.047   2151
  Dihedral  :  6.097  61.626   1685
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 1.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  8.91 %
    Favored  : 90.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.54 %
    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:  0.37 (0.21), residues: 1507
  helix:  0.81 (0.21), residues: 643
  sheet:  1.95 (0.41), residues: 174
  loop : -0.72 (0.22), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 331 
 TYR   0.016   0.001   TYR C 221 
 PHE   0.014   0.001   PHE C 355 
 TRP   0.019   0.001   TRP B 327 
 HIS   0.006   0.001   HIS B 289 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 (12334)
  covalent geometry    : angle       0.50681 /  0.26 (16741)
  SS BOND              : bond        0.00585 /  0.31 (    1)
  SS BOND              : angle       3.77147 /  2.22 (    2)
  hydrogen bonds       : bond        0.05045 /  3.45 (  459)
  hydrogen bonds       : angle       4.06929 /  2.93 ( 1290)

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

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

  3014 Ramachandran restraints generated.
    1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3014 Ramachandran restraints generated.
    1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.404 
Fit side-chains
REVERT: A   32 ARG cc_start: 0.8416 (tpp-160) cc_final: 0.8176 (ttm110)
REVERT: A  150 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7883 (mp0)
REVERT: A  359 MET cc_start: 0.7659 (tpt) cc_final: 0.7375 (tpt)
REVERT: C   71 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8044 (mp0)
REVERT: C   86 ASP cc_start: 0.7972 (m-30) cc_final: 0.7719 (m-30)
REVERT: C  189 GLN cc_start: 0.8270 (mt0) cc_final: 0.8049 (mm110)
  outliers start: 13
  outliers final: 5
  residues processed: 124
  average time/residue: 0.6575
  time to fit residues: 86.8561
Evaluate side-chains
  119 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 112
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain C residue   71 GLU
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain E residue   75 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 66 optimal weight:    9.9990
   chunk 80 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 126 optimal weight:    5.9990
   chunk 85 optimal weight:    0.8980
   chunk 132 optimal weight:    6.9990
   chunk 90 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0980
   chunk 57 optimal weight:    2.9990
   chunk 115 optimal weight:    1.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 292 ASN
E  77 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.128276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.094487 restraints weight = 34786.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 2.95
r_work: 0.2929 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2894
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2894 r_free = 0.2894    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2894 r_free = 0.2894    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 8 (14 function evaluations)
r_final: 0.2894
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8934
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12335  Z= 0.089
  Angle     :  0.463   9.739  16743  Z= 0.238
  Chirality :  0.041   0.141   1881
  Planarity :  0.004   0.046   2151
  Dihedral  :  5.906  59.980   1685
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 2.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  9.38 %
    Favored  : 89.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.54 %
    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 (0.21), residues: 1507
  helix:  0.96 (0.21), residues: 641
  sheet:  1.99 (0.40), residues: 180
  loop : -0.66 (0.22), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 331 
 TYR   0.010   0.001   TYR A 221 
 PHE   0.010   0.001   PHE C 355 
 TRP   0.021   0.001   TRP B 327 
 HIS   0.004   0.001   HIS B 289 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00189 /  0.09 (12334)
  covalent geometry    : angle       0.46168 /  0.24 (16741)
  SS BOND              : bond        0.00613 /  0.32 (    1)
  SS BOND              : angle       2.64670 /  1.56 (    2)
  hydrogen bonds       : bond        0.03762 /  2.57 (  459)
  hydrogen bonds       : angle       3.88909 /  2.82 ( 1290)

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

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

  3014 Ramachandran restraints generated.
    1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3014 Ramachandran restraints generated.
    1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 0.469 
Fit side-chains
REVERT: A   32 ARG cc_start: 0.8189 (tpp-160) cc_final: 0.7939 (ttm110)
REVERT: A  150 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7785 (mp0)
REVERT: C   86 ASP cc_start: 0.7951 (m-30) cc_final: 0.7689 (m-30)
REVERT: C  189 GLN cc_start: 0.8099 (mt0) cc_final: 0.7883 (mm110)
  outliers start: 10
  outliers final: 5
  residues processed: 123
  average time/residue: 0.7214
  time to fit residues: 94.8406
Evaluate side-chains
  119 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain D residue   89 GLN
Chi-restraints excluded: chain D residue  131 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 9 optimal weight:    9.9990
   chunk 52 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0970
   chunk 148 optimal weight:   30.0000
   chunk 68 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 28 optimal weight:    8.9990
   chunk 4 optimal weight:    6.9990
   chunk 103 optimal weight:    1.9990
   overall best weight:    1.7784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 292 ASN
E  77 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.125960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.091450 restraints weight = 35219.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 3.04
r_work: 0.2878 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2871
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2871 r_free = 0.2871    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2871 r_free = 0.2871    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (12 function evaluations)
r_final: 0.2871
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9023
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12335  Z= 0.130
  Angle     :  0.506  10.458  16743  Z= 0.262
  Chirality :  0.042   0.158   1881
  Planarity :  0.004   0.044   2151
  Dihedral  :  5.982  61.195   1685
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  9.15 %
    Favored  : 89.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.54 %
    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:  0.45 (0.21), residues: 1507
  helix:  0.92 (0.21), residues: 643
  sheet:  1.93 (0.41), residues: 174
  loop : -0.70 (0.22), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 331 
 TYR   0.015   0.001   TYR C 221 
 PHE   0.015   0.001   PHE C 355 
 TRP   0.019   0.001   TRP B 327 
 HIS   0.006   0.001   HIS B 289 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.13 (12334)
  covalent geometry    : angle       0.50547 /  0.26 (16741)
  SS BOND              : bond        0.00719 /  0.38 (    1)
  SS BOND              : angle       2.63590 /  1.55 (    2)
  hydrogen bonds       : bond        0.04956 /  3.39 (  459)
  hydrogen bonds       : angle       4.01344 /  2.90 ( 1290)

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

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

  3014 Ramachandran restraints generated.
    1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3014 Ramachandran restraints generated.
    1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 ARG cc_start: 0.8292 (tpp-160) cc_final: 0.8052 (ttm110)
REVERT: A  150 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7834 (mp0)
REVERT: A  359 MET cc_start: 0.7614 (tpt) cc_final: 0.7358 (tpt)
REVERT: C   71 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7910 (mp0)
REVERT: C   86 ASP cc_start: 0.7987 (m-30) cc_final: 0.7731 (m-30)
REVERT: C  189 GLN cc_start: 0.8204 (mt0) cc_final: 0.7992 (mm110)
  outliers start: 12
  outliers final: 8
  residues processed: 124
  average time/residue: 0.7799
  time to fit residues: 103.1866
Evaluate side-chains
  125 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   71 GLU
Chi-restraints excluded: chain D residue   89 GLN
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  174 GLU
Chi-restraints excluded: chain D residue  240 SER
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain D residue  359 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 86 optimal weight:    3.9990
   chunk 146 optimal weight:   30.0000
   chunk 60 optimal weight:    4.9990
   chunk 147 optimal weight:    7.9990
   chunk 4 optimal weight:    8.9990
   chunk 39 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0010
   overall best weight:    2.9994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 292 ASN
D 122 HIS
E  21 GLN
E  77 HIS
E  78 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.123630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.089075 restraints weight = 30462.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 2.56
r_work: 0.2858 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2735 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2727
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2727 r_free = 0.2727    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2727 r_free = 0.2727    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 8 (17 function evaluations)
r_final: 0.2727
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9101
moved from start:          0.1646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  12335  Z= 0.194
  Angle     :  0.589  10.712  16743  Z= 0.304
  Chirality :  0.045   0.179   1881
  Planarity :  0.005   0.045   2151
  Dihedral  :  6.286  64.710   1685
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 2.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  9.38 %
    Favored  : 89.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.54 %
    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:  0.26 (0.21), residues: 1507
  helix:  0.75 (0.21), residues: 644
  sheet:  1.83 (0.40), residues: 174
  loop : -0.81 (0.21), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  91 
 TYR   0.018   0.002   TYR C 221 
 PHE   0.021   0.002   PHE C 355 
 TRP   0.017   0.001   TRP B 327 
 HIS   0.007   0.002   HIS B 289 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00473 /  0.19 (12334)
  covalent geometry    : angle       0.58851 /  0.30 (16741)
  SS BOND              : bond        0.00618 /  0.33 (    1)
  SS BOND              : angle       2.83294 /  1.67 (    2)
  hydrogen bonds       : bond        0.06316 /  4.32 (  459)
  hydrogen bonds       : angle       4.24095 /  3.05 ( 1290)

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

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

  3014 Ramachandran restraints generated.
    1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3014 Ramachandran restraints generated.
    1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 ARG cc_start: 0.8466 (tpp-160) cc_final: 0.8253 (ttm110)
REVERT: A  114 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7843 (mm-30)
REVERT: A  150 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7944 (mp0)
REVERT: A  359 MET cc_start: 0.7742 (tpt) cc_final: 0.7385 (tpt)
REVERT: C   71 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8093 (mp0)
REVERT: C   86 ASP cc_start: 0.7991 (m-30) cc_final: 0.7735 (m-30)
REVERT: C  189 GLN cc_start: 0.8319 (mt0) cc_final: 0.8108 (mm110)
REVERT: D  251 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8573 (mtmt)
  outliers start: 14
  outliers final: 5
  residues processed: 127
  average time/residue: 0.7519
  time to fit residues: 101.8067
Evaluate side-chains
  126 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain C residue   71 GLU
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  240 SER
Chi-restraints excluded: chain D residue  251 LYS
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain D residue  359 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 74 optimal weight:    6.9990
   chunk 134 optimal weight:    0.8980
   chunk 140 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    1.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 292 ASN
C 298 ASN
E  21 GLN
E  77 HIS
E  78 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.126060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.091895 restraints weight = 34950.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 2.94
r_work: 0.2889 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2873
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2873 r_free = 0.2873    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2873 r_free = 0.2873    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 7 (15 function evaluations)
r_final: 0.2873
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8982
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12335  Z= 0.114
  Angle     :  0.500  10.940  16743  Z= 0.259
  Chirality :  0.042   0.151   1881
  Planarity :  0.004   0.043   2151
  Dihedral  :  6.157  64.170   1685
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 2.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  9.93 %
    Favored  : 89.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.54 %
    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:  0.38 (0.21), residues: 1507
  helix:  0.88 (0.21), residues: 643
  sheet:  1.90 (0.41), residues: 174
  loop : -0.76 (0.21), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C  91 
 TYR   0.012   0.001   TYR C 221 
 PHE   0.013   0.001   PHE C 355 
 TRP   0.020   0.001   TRP B 327 
 HIS   0.006   0.001   HIS B 289 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.11 (12334)
  covalent geometry    : angle       0.49894 /  0.26 (16741)
  SS BOND              : bond        0.00522 /  0.27 (    1)
  SS BOND              : angle       2.41232 /  1.42 (    2)
  hydrogen bonds       : bond        0.04652 /  3.17 (  459)
  hydrogen bonds       : angle       4.05213 /  2.92 ( 1290)

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

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

  3014 Ramachandran restraints generated.
    1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3014 Ramachandran restraints generated.
    1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 ARG cc_start: 0.8230 (tpp-160) cc_final: 0.8008 (ttm110)
REVERT: A  114 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7547 (mm-30)
REVERT: A  150 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7783 (mp0)
REVERT: C   71 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7865 (mp0)
REVERT: C   86 ASP cc_start: 0.7973 (m-30) cc_final: 0.7716 (m-30)
REVERT: C  189 GLN cc_start: 0.8120 (mt0) cc_final: 0.7903 (mm110)
  outliers start: 9
  outliers final: 3
  residues processed: 124
  average time/residue: 0.8006
  time to fit residues: 105.4611
Evaluate side-chains
  123 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain C residue   71 GLU
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  359 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 127 optimal weight:    0.9990
   chunk 70 optimal weight:    0.0970
   chunk 108 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 83 optimal weight:    0.7980
   chunk 109 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0170
   chunk 84 optimal weight:    1.9990
   chunk 147 optimal weight:   20.0000
   overall best weight:    0.7820

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 292 ASN
C 298 ASN
E  21 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.128508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.094599 restraints weight = 28726.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 2.49
r_work: 0.2934 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2812 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2790
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.2790
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9024
moved from start:          0.1746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12335  Z= 0.090
  Angle     :  0.469  11.197  16743  Z= 0.239
  Chirality :  0.041   0.142   1881
  Planarity :  0.004   0.043   2151
  Dihedral  :  5.871  61.108   1685
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 2.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 10.40 %
    Favored  : 89.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.54 %
    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:  0.51 (0.21), residues: 1507
  helix:  1.00 (0.21), residues: 643
  sheet:  1.94 (0.41), residues: 169
  loop : -0.69 (0.22), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C  91 
 TYR   0.010   0.001   TYR A 221 
 PHE   0.008   0.001   PHE C 355 
 TRP   0.020   0.001   TRP B 327 
 HIS   0.004   0.001   HIS B 289 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00196 /  0.09 (12334)
  covalent geometry    : angle       0.46890 /  0.24 (16741)
  SS BOND              : bond        0.00525 /  0.28 (    1)
  SS BOND              : angle       2.07852 /  1.22 (    2)
  hydrogen bonds       : bond        0.03658 /  2.49 (  459)
  hydrogen bonds       : angle       3.83850 /  2.78 ( 1290)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3985.55 seconds
wall clock time: 68 minutes 30.65 seconds (4110.65 seconds total)