Starting phenix.real_space_refine
on Wed Sep 17 13:45:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fee_50339/09_2025/9fee_50339.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fee_50339/09_2025/9fee_50339.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fee_50339/09_2025/9fee_50339.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fee_50339/09_2025/9fee_50339.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fee_50339/09_2025/9fee_50339.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fee_50339/09_2025/9fee_50339.cif"
  }
  resolution = 3.03
  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=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    5818      2.51       5
     N    1568      2.21       5
     O    1678      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9112
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2291
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2291
          Classifications: {'peptide': 311}
          Link IDs: {'PTRANS': 21, 'TRANS': 289}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2267
          Classifications: {'peptide': 308}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 286}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2262
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2262
          Classifications: {'peptide': 307}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 285}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2292
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 310, 2286
          Classifications: {'peptide': 310}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 288}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 310, 2286
          Classifications: {'peptide': 310}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 288}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 2318
  Time building chain proxies: 2.77, per 1000 atoms: 0.30
  Number of scatterers: 9112
  At special positions: 0
  Unit cell: (91.16, 103.2, 103.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    1678      8.00
     N    1568      7.00
     C    5818      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.91
  Conformation dependent library (CDL) restraints added in 465.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2242

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 12 sheets defined
      48.5% alpha, 12.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 23
      removed outlier: 3.607A  pdb=" N   GLN A  15 " --> pdb=" O   GLY A  11 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   SER A  16 " --> pdb=" O   GLY A  12 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ARG A  23 " --> pdb=" O   LEU A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 47
    Processing helix  chain 'A' and resid 69 through 76
    Processing helix  chain 'A' and resid 98 through 116
      removed outlier: 4.077A  pdb=" N   VAL A 102 " --> pdb=" O   ASP A  98 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   SER A 116 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 145
      Proline residue:  A 135  - end of helix
    Processing helix  chain 'A' and resid 156 through 171
      removed outlier: 4.283A  pdb=" N   GLY A 160 " --> pdb=" O   SER A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 225
      removed outlier: 3.508A  pdb=" N   ILE A 210 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
      removed outlier: 5.472A  pdb=" N   GLY A 218 " --> pdb=" O   VAL A 214 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   THR A 219 " --> pdb=" O   GLN A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 251
      removed outlier: 3.521A  pdb=" N   GLU A 237 " --> pdb=" O   LEU A 233 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ALA A 238 " --> pdb=" O   SER A 234 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLY A 239 " --> pdb=" O   MET A 235 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA A 240 " --> pdb=" O   ALA A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 319
      removed outlier: 3.578A  pdb=" N   GLU A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   VAL A 307 " --> pdb=" O   GLU A 303 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LYS A 310 " --> pdb=" O   GLY A 306 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ALA A 313 " --> pdb=" O   LYS A 309 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LYS A 314 " --> pdb=" O   LYS A 310 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ALA A 319 " --> pdb=" O   GLY A 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 25
      removed outlier: 3.806A  pdb=" N   SER B  16 " --> pdb=" O   GLY B  12 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ARG B  23 " --> pdb=" O   LEU B  19 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLU B  24 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 47
      removed outlier: 3.830A  pdb=" N   ASP B  45 " --> pdb=" O   GLY B  41 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU B  46 " --> pdb=" O   VAL B  42 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   SER B  47 " --> pdb=" O   ALA B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 76
      removed outlier: 3.759A  pdb=" N   THR B  73 " --> pdb=" O   ASP B  69 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   GLU B  74 " --> pdb=" O   PRO B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 118
      removed outlier: 3.676A  pdb=" N   GLY B 105 " --> pdb=" O   ASN B 101 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   VAL B 117 " --> pdb=" O   THR B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 145
      Proline residue:  B 135  - end of helix
      removed outlier: 3.505A  pdb=" N   ALA B 138 " --> pdb=" O   THR B 134 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE B 144 " --> pdb=" O   THR B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 150
      No H-bonds generated for 'chain 'B' and resid 148 through 150'
    Processing helix  chain 'B' and resid 156 through 169
      removed outlier: 4.402A  pdb=" N   GLY B 160 " --> pdb=" O   SER B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 216
      removed outlier: 3.640A  pdb=" N   GLN B 215 " --> pdb=" O   ARG B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 225
      removed outlier: 3.949A  pdb=" N   VAL B 221 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   VAL B 222 " --> pdb=" O   GLY B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 252
      removed outlier: 3.684A  pdb=" N   MET B 235 " --> pdb=" O   ALA B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 319
      removed outlier: 3.800A  pdb=" N   GLY B 306 " --> pdb=" O   GLU B 302 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   VAL B 307 " --> pdb=" O   GLU B 303 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LYS B 310 " --> pdb=" O   GLY B 306 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   PHE B 318 " --> pdb=" O   LYS B 314 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   ALA B 319 " --> pdb=" O   GLY B 315 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 11 through 23
      removed outlier: 4.163A  pdb=" N   SER C  16 " --> pdb=" O   GLY C  12 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ARG C  23 " --> pdb=" O   LEU C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 38 through 47
      removed outlier: 3.715A  pdb=" N   ASP C  45 " --> pdb=" O   GLY C  41 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU C  46 " --> pdb=" O   VAL C  42 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   SER C  47 " --> pdb=" O   ALA C  43 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 76
      removed outlier: 3.596A  pdb=" N   THR C  73 " --> pdb=" O   ASP C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 115
      removed outlier: 3.573A  pdb=" N   ILE C 106 " --> pdb=" O   VAL C 102 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ASP C 109 " --> pdb=" O   GLY C 105 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU C 112 " --> pdb=" O   MET C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 145
      Proline residue:  C 135  - end of helix
      removed outlier: 3.560A  pdb=" N   LYS C 143 " --> pdb=" O   GLN C 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 156 through 171
      removed outlier: 4.347A  pdb=" N   GLY C 160 " --> pdb=" O   SER C 156 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ALA C 170 " --> pdb=" O   PHE C 166 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 194 through 197
      removed outlier: 3.856A  pdb=" N   ILE C 197 " --> pdb=" O   TYR C 194 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 194 through 197'
    Processing helix  chain 'C' and resid 206 through 216
    Processing helix  chain 'C' and resid 216 through 225
      removed outlier: 3.503A  pdb=" N   GLU C 220 " --> pdb=" O   VAL C 216 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   VAL C 221 " --> pdb=" O   ALA C 217 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL C 222 " --> pdb=" O   GLY C 218 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 232 through 251
      removed outlier: 3.698A  pdb=" N   HIS C 245 " --> pdb=" O   ARG C 241 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 294 through 318
      removed outlier: 3.599A  pdb=" N   GLY C 306 " --> pdb=" O   GLU C 302 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 11 through 25
      removed outlier: 4.013A  pdb=" N   SER D  16 " --> pdb=" O   GLY D  12 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ARG D  23 " --> pdb=" O   LEU D  19 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 38 through 47
      removed outlier: 3.850A  pdb=" N   ASP D  45 " --> pdb=" O   GLY D  41 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU D  46 " --> pdb=" O   VAL D  42 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   SER D  47 " --> pdb=" O   ALA D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 70 through 76
      removed outlier: 3.857A  pdb=" N   GLU D  74 " --> pdb=" O   PRO D  70 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LEU D  75 " --> pdb=" O   ALA D  71 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ALA D  76 " --> pdb=" O   LEU D  72 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 70 through 76'
    Processing helix  chain 'D' and resid 100 through 118
      removed outlier: 3.614A  pdb=" N   GLY D 105 " --> pdb=" O   ASN D 101 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ILE D 106 " --> pdb=" O   VAL D 102 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   SER D 116 " --> pdb=" O   LEU D 112 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   VAL D 117 " --> pdb=" O   THR D 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 145
      Proline residue:  D 135  - end of helix
      removed outlier: 3.692A  pdb=" N   ILE D 144 " --> pdb=" O   THR D 140 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 148 through 150
      No H-bonds generated for 'chain 'D' and resid 148 through 150'
    Processing helix  chain 'D' and resid 157 through 169
    Processing helix  chain 'D' and resid 206 through 225
      removed outlier: 3.802A  pdb=" N   GLN D 215 " --> pdb=" O   ARG D 211 " (cutoff:3.500A)
      removed outlier: 5.569A  pdb=" N   GLY D 218 " --> pdb=" O   VAL D 214 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   THR D 219 " --> pdb=" O   GLN D 215 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLU D 220 " --> pdb=" O   VAL D 216 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 231 through 252
      removed outlier: 3.533A  pdb=" N   MET D 235 " --> pdb=" O   ALA D 231 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   HIS D 245 " --> pdb=" O   ARG D 241 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   VAL D 246 " --> pdb=" O   PHE D 242 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 294 through 317
      removed outlier: 3.811A  pdb=" N   MET D 300 " --> pdb=" O   VAL D 296 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLY D 306 " --> pdb=" O   GLU D 302 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   LYS D 310 " --> pdb=" O   GLY D 306 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 60
      removed outlier: 6.292A  pdb=" N   LEU A  31 " --> pdb=" O   LYS A  57 " (cutoff:3.500A)
      removed outlier: 8.013A  pdb=" N   ALA A  59 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   LEU A  33 " --> pdb=" O   ALA A  59 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   ASN A   3 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   VAL A  83 " --> pdb=" O   ASN A   3 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA A   5 " --> pdb=" O   VAL A  83 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   PHE A 123 " --> pdb=" O   LEU A 153 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183
    Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 260
      removed outlier: 3.878A  pdb=" N   ALA A 260 " --> pdb=" O   MET A 275 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   MET A 275 " --> pdb=" O   ALA A 260 " (cutoff:3.500A)
      removed outlier: 5.245A  pdb=" N   ARG A 287 " --> pdb=" O   PRO A 276 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   VAL A 278 " --> pdb=" O   GLU A 285 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 55 through 59
      removed outlier: 3.690A  pdb=" N   LEU B  33 " --> pdb=" O   LYS B  57 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   PHE B  82 " --> pdb=" O   CYS B 124 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 181 through 183
    Processing sheet with id=AA6, first strand: chain 'B' and resid 257 through 261
      removed outlier: 3.778A  pdb=" N   ALA B 260 " --> pdb=" O   MET B 275 " (cutoff:3.500A)
      removed outlier: 5.259A  pdb=" N   ARG B 287 " --> pdb=" O   PRO B 276 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   VAL B 278 " --> pdb=" O   GLU B 285 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 55 through 60
      removed outlier: 6.325A  pdb=" N   LEU C  31 " --> pdb=" O   LYS C  57 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   ALA C  59 " --> pdb=" O   LEU C  31 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   LEU C  33 " --> pdb=" O   ALA C  59 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   PHE C 123 " --> pdb=" O   LEU C 153 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 181 through 183
    Processing sheet with id=AA9, first strand: chain 'C' and resid 257 through 261
      removed outlier: 3.557A  pdb=" N   ALA C 260 " --> pdb=" O   MET C 275 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   ARG C 287 " --> pdb=" O   PRO C 276 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   VAL C 278 " --> pdb=" O   GLU C 285 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 55 through 59
      removed outlier: 3.964A  pdb=" N   LEU D  33 " --> pdb=" O   LYS D  57 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   PHE D 123 " --> pdb=" O   LEU D 153 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 181 through 183
    Processing sheet with id=AB3, first strand: chain 'D' and resid 257 through 261
      removed outlier: 3.577A  pdb=" N   ALA D 260 " --> pdb=" O   MET D 275 " (cutoff:3.500A)
      removed outlier: 5.038A  pdb=" N   ARG D 287 " --> pdb=" O   PRO D 276 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   VAL D 278 " --> pdb=" O   GLU D 285 " (cutoff:3.500A)

    418 hydrogen bonds defined for protein.
    1236 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.51

  Time building geometry restraints manager: 1.19 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3006
        1.34 -     1.46: 1397
        1.46 -     1.58: 4786
        1.58 -     1.69: 0
        1.69 -     1.81: 80
  Bond restraints: 9269
  Sorted by residual:
  bond pdb=" C   HIS A 172 "
       pdb=" N   PRO A 173 "
    ideal  model  delta    sigma   weight residual
    1.332  1.354 -0.022 8.20e-03 1.49e+04 6.89e+00
  bond pdb=" N   PRO B  64 "
       pdb=" CA  PRO B  64 "
    ideal  model  delta    sigma   weight residual
    1.465  1.490 -0.025 2.03e-02 2.43e+03 1.53e+00
  bond pdb=" C   LEU B  63 "
       pdb=" N   PRO B  64 "
    ideal  model  delta    sigma   weight residual
    1.329  1.343 -0.014 1.18e-02 7.18e+03 1.44e+00
  bond pdb=" C   ARG C  68 "
       pdb=" N   ASP C  69 "
    ideal  model  delta    sigma   weight residual
    1.333  1.363 -0.031 2.74e-02 1.33e+03 1.26e+00
  bond pdb=" CG  GLU A 303 "
       pdb=" CD  GLU A 303 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 9.17e-01
  ... (remaining 9264 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 12293
        1.50 -     3.01: 274
        3.01 -     4.51: 41
        4.51 -     6.01: 16
        6.01 -     7.52: 6
  Bond angle restraints: 12630
  Sorted by residual:
  angle pdb=" C   GLU B 267 "
        pdb=" CA  GLU B 267 "
        pdb=" CB  GLU B 267 "
      ideal   model   delta    sigma   weight residual
     116.54  109.64    6.90 1.15e+00 7.56e-01 3.60e+01
  angle pdb=" CA  GLU B 267 "
        pdb=" C   GLU B 267 "
        pdb=" N   HIS B 268 "
      ideal   model   delta    sigma   weight residual
     119.52  116.27    3.25 7.90e-01 1.60e+00 1.69e+01
  angle pdb=" N   VAL C 126 "
        pdb=" CA  VAL C 126 "
        pdb=" C   VAL C 126 "
      ideal   model   delta    sigma   weight residual
     113.47  109.49    3.98 1.01e+00 9.80e-01 1.55e+01
  angle pdb=" C   VAL B 191 "
        pdb=" CA  VAL B 191 "
        pdb=" CB  VAL B 191 "
      ideal   model   delta    sigma   weight residual
     110.16  113.37   -3.21 1.01e+00 9.80e-01 1.01e+01
  angle pdb=" C   HIS D 185 "
        pdb=" N  BSER D 186 "
        pdb=" CA BSER D 186 "
      ideal   model   delta    sigma   weight residual
     121.54  115.61    5.93 1.91e+00 2.74e-01 9.65e+00
  ... (remaining 12625 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 4900
       17.85 -    35.69: 579
       35.69 -    53.54: 136
       53.54 -    71.39: 18
       71.39 -    89.23: 5
  Dihedral angle restraints: 5638
    sinusoidal: 2142
      harmonic: 3496
  Sorted by residual:
  dihedral pdb=" CA  PRO B  64 "
           pdb=" C   PRO B  64 "
           pdb=" N   PRO B  65 "
           pdb=" CA  PRO B  65 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.10  -26.90     0      5.00e+00 4.00e-02 2.89e+01
  dihedral pdb=" CA  PRO A  64 "
           pdb=" C   PRO A  64 "
           pdb=" N   PRO A  65 "
           pdb=" CA  PRO A  65 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.74  -25.26     0      5.00e+00 4.00e-02 2.55e+01
  dihedral pdb=" CA  LEU B  63 "
           pdb=" C   LEU B  63 "
           pdb=" N   PRO B  64 "
           pdb=" CA  PRO B  64 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.80  -25.20     0      5.00e+00 4.00e-02 2.54e+01
  ... (remaining 5635 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 764
       0.027 -    0.054: 471
       0.054 -    0.081: 159
       0.081 -    0.108: 121
       0.108 -    0.135: 44
  Chirality restraints: 1559
  Sorted by residual:
  chirality pdb=" CA  VAL C  66 "
            pdb=" N   VAL C  66 "
            pdb=" C   VAL C  66 "
            pdb=" CB  VAL C  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.56e-01
  chirality pdb=" CA  ASN A 128 "
            pdb=" N   ASN A 128 "
            pdb=" C   ASN A 128 "
            pdb=" CB  ASN A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.25e-01
  chirality pdb=" CA  ASN B 128 "
            pdb=" N   ASN B 128 "
            pdb=" C   ASN B 128 "
            pdb=" CB  ASN B 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.07e-01
  ... (remaining 1556 not shown)

  Planarity restraints: 1621
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C  66 "    0.028 5.00e-02 4.00e+02   4.28e-02 2.93e+00
        pdb=" N   PRO C  67 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO C  67 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C  67 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 191 "    0.028 5.00e-02 4.00e+02   4.26e-02 2.91e+00
        pdb=" N   PRO B 192 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 192 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 192 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  66 "   -0.026 5.00e-02 4.00e+02   3.96e-02 2.51e+00
        pdb=" N   PRO B  67 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B  67 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  67 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1618 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1490
        2.76 -     3.29: 8341
        3.29 -     3.83: 13738
        3.83 -     4.36: 16069
        4.36 -     4.90: 29062
  Nonbonded interactions: 68700
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 131 "
            pdb=" OG  SER B 186 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   LEU B 112 "
            pdb=" OG  SER B 116 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   SER A 156 "
            pdb=" OG  SER A 156 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   ALA D  76 "
            pdb=" OG  SER D 118 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" O   ALA A 313 "
            pdb=" OG1 THR A 317 "
     model   vdw
     2.266 3.040
  ... (remaining 68695 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 1 through 88 or resid 100 through 185 or resid 187 through \ 
 318))
  selection = (chain 'B' and (resid 1 through 185 or resid 187 through 318))
  selection = (chain 'C' and (resid 1 through 185 or resid 187 through 318))
  selection = (chain 'D' and (resid 1 through 88 or resid 100 through 185 or resid 187 through \ 
 318))
}

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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.460
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
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      :  0.004   0.045   9269  Z= 0.154
  Angle     :  0.582   7.517  12630  Z= 0.311
  Chirality :  0.046   0.135   1559
  Planarity :  0.005   0.043   1621
  Dihedral  : 15.800  89.231   3396
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 25.55 %
    Favored  : 74.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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 aren not related in a simple way.
  whole: -1.40 (0.23), residues: 1223
  helix:  0.10 (0.22), residues: 534
  sheet: -1.24 (0.42), residues: 151
  loop : -1.88 (0.26), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 142 
 TYR   0.010   0.001   TYR D 261 
 PHE   0.012   0.001   PHE D  27 
 HIS   0.003   0.001   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 9269)
  covalent geometry    : angle       0.58250 (12630)
  hydrogen bonds       : bond        0.29648 (  418)
  hydrogen bonds       : angle       7.05346 ( 1236)

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.400 
Fit side-chains
REVERT: B  263 ASP cc_start: 0.7936 (t70) cc_final: 0.7667 (t70)
  outliers start: 2
  outliers final: 1
  residues processed: 78
  average time/residue: 0.0904
  time to fit residues: 10.3256
Evaluate side-chains
  74 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  247 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.3980
   chunk 117 optimal weight:    0.0870
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
B 169 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.123497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.102552 restraints weight = 18208.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.77
r_work: 0.3136 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3139
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3139 r_free = 0.3139    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3139 r_free = 0.3139    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3139
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.1391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9269  Z= 0.126
  Angle     :  0.568   5.764  12630  Z= 0.299
  Chirality :  0.045   0.151   1559
  Planarity :  0.005   0.044   1621
  Dihedral  :  4.461  29.032   1308
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 22.03 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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 aren not related in a simple way.
  whole: -0.36 (0.24), residues: 1223
  helix:  1.27 (0.23), residues: 538
  sheet: -0.65 (0.43), residues: 151
  loop : -1.73 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 287 
 TYR   0.008   0.001   TYR D 261 
 PHE   0.009   0.001   PHE D  27 
 HIS   0.003   0.001   HIS C 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 9269)
  covalent geometry    : angle       0.56752 (12630)
  hydrogen bonds       : bond        0.05448 (  418)
  hydrogen bonds       : angle       4.49229 ( 1236)

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 86
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: B    7 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.7887 (mm)
REVERT: B   30 THR cc_start: 0.8553 (t) cc_final: 0.8330 (m)
REVERT: C  219 THR cc_start: 0.8183 (m) cc_final: 0.7946 (p)
REVERT: C  303 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.8028 (mp0)
REVERT: D   51 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.7616 (tpt-90)
REVERT: D  169 ASN cc_start: 0.8838 (m-40) cc_final: 0.8542 (m110)
  outliers start: 29
  outliers final: 11
  residues processed: 109
  average time/residue: 0.0867
  time to fit residues: 13.7057
Evaluate side-chains
  92 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   57 LYS
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  101 ASN
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain D residue   50 ASP
Chi-restraints excluded: chain D residue   51 ARG
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  237 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 17 optimal weight:    0.3980
   chunk 54 optimal weight:    0.7980
   chunk 32 optimal weight:    6.9990
   chunk 98 optimal weight:    0.0870
   chunk 46 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 74 optimal weight:    5.9990
   chunk 103 optimal weight:    6.9990
   chunk 66 optimal weight:    7.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    1.4560

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

Flipped N/Q/H residues before XYZ refinement:
C 150 ASN
D 185 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.121916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.098490 restraints weight = 32448.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 3.72
r_work: 0.3052 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3056
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3056
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.1456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9269  Z= 0.130
  Angle     :  0.557   6.132  12630  Z= 0.291
  Chirality :  0.045   0.136   1559
  Planarity :  0.005   0.043   1621
  Dihedral  :  4.412  27.883   1307
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 21.73 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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 aren not related in a simple way.
  whole: -0.10 (0.25), residues: 1223
  helix:  1.61 (0.23), residues: 540
  sheet: -0.55 (0.42), residues: 156
  loop : -1.77 (0.26), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 287 
 TYR   0.007   0.001   TYR C 261 
 PHE   0.010   0.001   PHE D  27 
 HIS   0.013   0.001   HIS D 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 9269)
  covalent geometry    : angle       0.55696 (12630)
  hydrogen bonds       : bond        0.05309 (  418)
  hydrogen bonds       : angle       4.20587 ( 1236)

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 83
  time to evaluate  : 0.376 
Fit side-chains
REVERT: B    7 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.7880 (mm)
REVERT: B   68 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.6253 (mtp180)
REVERT: B   74 GLU cc_start: 0.7791 (pm20) cc_final: 0.6699 (tp30)
REVERT: B   77 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7102 (mp0)
REVERT: C  303 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7960 (mp0)
REVERT: D   51 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.7585 (tpt-90)
REVERT: D  169 ASN cc_start: 0.8904 (m-40) cc_final: 0.8670 (m110)
  outliers start: 35
  outliers final: 22
  residues processed: 111
  average time/residue: 0.0974
  time to fit residues: 15.4668
Evaluate side-chains
  103 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 76
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   57 LYS
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  159 ASP
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  228 ARG
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   68 ARG
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  263 ASP
Chi-restraints excluded: chain B residue  302 GLU
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain D residue   51 ARG
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  153 LEU
Chi-restraints excluded: chain D residue  159 ASP
Chi-restraints excluded: chain D residue  237 GLU
Chi-restraints excluded: chain D residue  275 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 31 optimal weight:    8.9990
   chunk 100 optimal weight:    4.9990
   chunk 78 optimal weight:    7.9990
   chunk 99 optimal weight:    8.9990
   chunk 54 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 105 optimal weight:    8.9990
   chunk 51 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 169 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.118192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.097101 restraints weight = 18478.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3169 rms_B_bonded: 2.72
r_work: 0.3053 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3056
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3056
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.1385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   9269  Z= 0.200
  Angle     :  0.630   6.730  12630  Z= 0.330
  Chirality :  0.048   0.150   1559
  Planarity :  0.005   0.044   1621
  Dihedral  :  4.766  27.319   1307
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 21.83 %
    Favored  : 73.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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 aren not related in a simple way.
  whole: -0.35 (0.24), residues: 1223
  helix:  1.45 (0.23), residues: 540
  sheet: -0.66 (0.39), residues: 176
  loop : -2.00 (0.27), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  23 
 TYR   0.010   0.001   TYR D 259 
 PHE   0.013   0.002   PHE A  27 
 HIS   0.004   0.001   HIS D 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 9269)
  covalent geometry    : angle       0.63011 (12630)
  hydrogen bonds       : bond        0.06541 (  418)
  hydrogen bonds       : angle       4.37746 ( 1236)

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 77
  time to evaluate  : 0.374 
Fit side-chains
REVERT: B    7 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.7952 (mm)
REVERT: B   74 GLU cc_start: 0.7745 (pm20) cc_final: 0.6796 (tp30)
REVERT: B   77 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7053 (mp0)
REVERT: B  267 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7821 (mp0)
REVERT: B  293 ILE cc_start: 0.9261 (pt) cc_final: 0.8982 (pt)
REVERT: C  303 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.8029 (mp0)
REVERT: D    7 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.7914 (mm)
REVERT: D   51 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.7630 (tpt-90)
REVERT: D  169 ASN cc_start: 0.8943 (m-40) cc_final: 0.8691 (m110)
  outliers start: 42
  outliers final: 25
  residues processed: 111
  average time/residue: 0.1022
  time to fit residues: 15.9827
Evaluate side-chains
  105 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 74
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   57 LYS
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  159 ASP
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  228 ARG
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  263 ASP
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain B residue  302 GLU
Chi-restraints excluded: chain C residue  131 ASN
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain D residue    7 ILE
Chi-restraints excluded: chain D residue   51 ARG
Chi-restraints excluded: chain D residue   55 THR
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  153 LEU
Chi-restraints excluded: chain D residue  159 ASP
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  275 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 86 optimal weight:    8.9990
   chunk 3 optimal weight:    1.9990
   chunk 104 optimal weight:    4.9990
   chunk 54 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 119 optimal weight:    9.9990
   chunk 107 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0980
   chunk 101 optimal weight:    8.9990
   chunk 48 optimal weight:    5.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.121900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.098632 restraints weight = 31114.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 3.64
r_work: 0.3056 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3060
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3060
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9269  Z= 0.123
  Angle     :  0.555   6.972  12630  Z= 0.289
  Chirality :  0.045   0.139   1559
  Planarity :  0.005   0.045   1621
  Dihedral  :  4.537  28.111   1307
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 22.54 %
    Favored  : 74.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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 aren not related in a simple way.
  whole: -0.08 (0.25), residues: 1223
  helix:  1.71 (0.23), residues: 541
  sheet: -0.57 (0.43), residues: 151
  loop : -1.85 (0.26), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  51 
 TYR   0.007   0.001   TYR D 261 
 PHE   0.011   0.001   PHE D  27 
 HIS   0.002   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9269)
  covalent geometry    : angle       0.55492 (12630)
  hydrogen bonds       : bond        0.04671 (  418)
  hydrogen bonds       : angle       4.08961 ( 1236)

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 85
  time to evaluate  : 0.361 
Fit side-chains
REVERT: B    7 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.7925 (mm)
REVERT: B   68 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.6274 (mtp180)
REVERT: B   74 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6844 (tp30)
REVERT: B   77 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7084 (mp0)
REVERT: B  267 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7897 (mp0)
REVERT: C  303 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7990 (mp0)
REVERT: D   51 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.7591 (tpt-90)
REVERT: D  169 ASN cc_start: 0.8891 (m-40) cc_final: 0.8677 (m110)
  outliers start: 32
  outliers final: 21
  residues processed: 108
  average time/residue: 0.1064
  time to fit residues: 16.0445
Evaluate side-chains
  105 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 77
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  159 ASP
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  228 ARG
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   68 ARG
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  263 ASP
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain B residue  302 GLU
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain D residue   51 ARG
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  153 LEU
Chi-restraints excluded: chain D residue  237 GLU
Chi-restraints excluded: chain D residue  275 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 86 optimal weight:   10.0000
   chunk 20 optimal weight:    4.9990
   chunk 5 optimal weight:    7.9990
   chunk 16 optimal weight:    0.0670
   chunk 35 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   overall best weight:    2.2126

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

Flipped N/Q/H residues before XYZ refinement:
** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.119874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.097822 restraints weight = 23703.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 3.14
r_work: 0.3056 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3058
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3058 r_free = 0.3058    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3058 r_free = 0.3058    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3058
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.1593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9269  Z= 0.156
  Angle     :  0.584   7.551  12630  Z= 0.304
  Chirality :  0.046   0.136   1559
  Planarity :  0.005   0.043   1621
  Dihedral  :  4.605  27.542   1307
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 22.54 %
    Favored  : 73.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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 aren not related in a simple way.
  whole: -0.14 (0.25), residues: 1223
  helix:  1.69 (0.23), residues: 541
  sheet: -0.60 (0.40), residues: 166
  loop : -1.95 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 162 
 TYR   0.008   0.001   TYR C 261 
 PHE   0.012   0.001   PHE D  27 
 HIS   0.003   0.001   HIS D 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 9269)
  covalent geometry    : angle       0.58433 (12630)
  hydrogen bonds       : bond        0.05394 (  418)
  hydrogen bonds       : angle       4.17600 ( 1236)

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 78
  time to evaluate  : 0.365 
Fit side-chains
REVERT: B    7 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.7895 (mm)
REVERT: B   68 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.6253 (mtp180)
REVERT: B   74 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6990 (tp30)
REVERT: B   77 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7187 (mp0)
REVERT: B  267 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7880 (mp0)
REVERT: B  293 ILE cc_start: 0.9271 (pt) cc_final: 0.9010 (pt)
REVERT: C  303 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.8003 (mp0)
REVERT: D    7 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.7851 (mm)
REVERT: D   51 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.7644 (tpt-90)
REVERT: D  169 ASN cc_start: 0.8936 (m-40) cc_final: 0.8710 (m110)
  outliers start: 40
  outliers final: 27
  residues processed: 109
  average time/residue: 0.0959
  time to fit residues: 14.8071
Evaluate side-chains
  111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 76
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  159 ASP
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  228 ARG
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   50 ASP
Chi-restraints excluded: chain B residue   68 ARG
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  263 ASP
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain B residue  302 GLU
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain C residue  230 SER
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain D residue    7 ILE
Chi-restraints excluded: chain D residue   51 ARG
Chi-restraints excluded: chain D residue   55 THR
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  153 LEU
Chi-restraints excluded: chain D residue  159 ASP
Chi-restraints excluded: chain D residue  248 LYS
Chi-restraints excluded: chain D residue  275 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 70 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   chunk 110 optimal weight:    3.9990
   chunk 61 optimal weight:   10.0000
   chunk 71 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 31 optimal weight:    8.9990
   chunk 54 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 169 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.119450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.096466 restraints weight = 31103.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 3.57
r_work: 0.3023 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3025
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3025 r_free = 0.3025    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3025 r_free = 0.3025    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3025
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9269  Z= 0.158
  Angle     :  0.591   7.846  12630  Z= 0.308
  Chirality :  0.047   0.137   1559
  Planarity :  0.005   0.044   1621
  Dihedral  :  4.680  27.575   1307
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 22.54 %
    Favored  : 73.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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 aren not related in a simple way.
  whole: -0.19 (0.25), residues: 1223
  helix:  1.65 (0.23), residues: 541
  sheet: -0.62 (0.40), residues: 166
  loop : -1.97 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  23 
 TYR   0.008   0.001   TYR D 261 
 PHE   0.012   0.001   PHE D  27 
 HIS   0.003   0.001   HIS D 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 9269)
  covalent geometry    : angle       0.59125 (12630)
  hydrogen bonds       : bond        0.05513 (  418)
  hydrogen bonds       : angle       4.18974 ( 1236)

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 77
  time to evaluate  : 0.320 
Fit side-chains
REVERT: B    7 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.7939 (mm)
REVERT: B   68 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.6313 (mtp180)
REVERT: B   74 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7047 (tp30)
REVERT: B   77 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7229 (mp0)
REVERT: B  267 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7878 (mp0)
REVERT: B  293 ILE cc_start: 0.9294 (pt) cc_final: 0.9041 (pt)
REVERT: C  303 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.8023 (mp0)
REVERT: D    7 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.7898 (mm)
REVERT: D   51 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.7623 (tpt-90)
REVERT: D  169 ASN cc_start: 0.8954 (m-40) cc_final: 0.8730 (m110)
  outliers start: 43
  outliers final: 29
  residues processed: 111
  average time/residue: 0.0920
  time to fit residues: 14.5880
Evaluate side-chains
  109 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 72
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  159 ASP
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   50 ASP
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   68 ARG
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  230 SER
Chi-restraints excluded: chain B residue  263 ASP
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain B residue  302 GLU
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain C residue  230 SER
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain D residue    7 ILE
Chi-restraints excluded: chain D residue   51 ARG
Chi-restraints excluded: chain D residue   55 THR
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  153 LEU
Chi-restraints excluded: chain D residue  159 ASP
Chi-restraints excluded: chain D residue  248 LYS
Chi-restraints excluded: chain D residue  275 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 117 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 70 optimal weight:    7.9990
   chunk 8 optimal weight:    7.9990
   chunk 77 optimal weight:    7.9990
   chunk 81 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 104 optimal weight:    0.6980
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.118420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.096431 restraints weight = 25529.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 3.13
r_work: 0.3032 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3035
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3035
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9269  Z= 0.179
  Angle     :  0.612   8.029  12630  Z= 0.319
  Chirality :  0.047   0.144   1559
  Planarity :  0.005   0.044   1621
  Dihedral  :  4.771  27.512   1307
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 22.84 %
    Favored  : 72.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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 aren not related in a simple way.
  whole: -0.29 (0.25), residues: 1223
  helix:  1.58 (0.23), residues: 541
  sheet: -0.67 (0.38), residues: 176
  loop : -2.06 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 211 
 TYR   0.008   0.001   TYR D 259 
 PHE   0.013   0.002   PHE D  27 
 HIS   0.004   0.001   HIS D 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 9269)
  covalent geometry    : angle       0.61218 (12630)
  hydrogen bonds       : bond        0.05928 (  418)
  hydrogen bonds       : angle       4.26844 ( 1236)

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 75
  time to evaluate  : 0.386 
Fit side-chains
REVERT: B    7 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.7973 (mm)
REVERT: B   68 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.6312 (mtp180)
REVERT: B   74 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6896 (tp30)
REVERT: B   77 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7164 (mp0)
REVERT: B  267 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7844 (mp0)
REVERT: B  293 ILE cc_start: 0.9276 (pt) cc_final: 0.9006 (pt)
REVERT: C   73 THR cc_start: 0.8722 (p) cc_final: 0.8495 (t)
REVERT: C  303 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8053 (mp0)
REVERT: D    7 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.7926 (mm)
REVERT: D   51 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.7640 (tpt-90)
REVERT: D  169 ASN cc_start: 0.8948 (m-40) cc_final: 0.8727 (m110)
  outliers start: 43
  outliers final: 29
  residues processed: 111
  average time/residue: 0.0988
  time to fit residues: 15.6839
Evaluate side-chains
  111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 74
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  159 ASP
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   50 ASP
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   68 ARG
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  230 SER
Chi-restraints excluded: chain B residue  263 ASP
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain B residue  302 GLU
Chi-restraints excluded: chain C residue  131 ASN
Chi-restraints excluded: chain C residue  230 SER
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain D residue    7 ILE
Chi-restraints excluded: chain D residue   51 ARG
Chi-restraints excluded: chain D residue   55 THR
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  153 LEU
Chi-restraints excluded: chain D residue  159 ASP
Chi-restraints excluded: chain D residue  248 LYS
Chi-restraints excluded: chain D residue  275 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 91 optimal weight:   10.0000
   chunk 17 optimal weight:    8.9990
   chunk 35 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 93 optimal weight:    0.3980
   chunk 98 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 119 optimal weight:    7.9990
   chunk 90 optimal weight:    0.8980
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.120489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.098491 restraints weight = 23697.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 3.13
r_work: 0.3066 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3069
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3069
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9269  Z= 0.133
  Angle     :  0.568   7.025  12630  Z= 0.295
  Chirality :  0.046   0.135   1559
  Planarity :  0.005   0.044   1621
  Dihedral  :  4.620  27.787   1307
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 23.04 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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 aren not related in a simple way.
  whole: -0.13 (0.25), residues: 1223
  helix:  1.70 (0.23), residues: 540
  sheet: -0.60 (0.40), residues: 166
  loop : -1.93 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 287 
 TYR   0.007   0.001   TYR C 261 
 PHE   0.011   0.001   PHE D  27 
 HIS   0.003   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 9269)
  covalent geometry    : angle       0.56798 (12630)
  hydrogen bonds       : bond        0.04912 (  418)
  hydrogen bonds       : angle       4.10270 ( 1236)

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 82
  time to evaluate  : 0.352 
Fit side-chains
REVERT: B    7 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.7875 (mm)
REVERT: B   68 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.6243 (mtp180)
REVERT: B   74 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7072 (tp30)
REVERT: B   77 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7214 (mp0)
REVERT: B  267 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7865 (mp0)
REVERT: B  293 ILE cc_start: 0.9276 (pt) cc_final: 0.9015 (pt)
REVERT: C  303 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.8016 (mp0)
REVERT: D    7 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.7850 (mm)
REVERT: D   51 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.7592 (tpt-90)
  outliers start: 37
  outliers final: 27
  residues processed: 112
  average time/residue: 0.0979
  time to fit residues: 15.6819
Evaluate side-chains
  108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 73
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   57 LYS
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  159 ASP
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   50 ASP
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   68 ARG
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  230 SER
Chi-restraints excluded: chain B residue  263 ASP
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain B residue  302 GLU
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain D residue    7 ILE
Chi-restraints excluded: chain D residue   51 ARG
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  153 LEU
Chi-restraints excluded: chain D residue  159 ASP
Chi-restraints excluded: chain D residue  248 LYS
Chi-restraints excluded: chain D residue  275 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 75 optimal weight:   10.0000
   chunk 50 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 22 optimal weight:    6.9990
   chunk 11 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 44 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 46 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.117623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.094548 restraints weight = 32270.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 3.61
r_work: 0.2992 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2995
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2995 r_free = 0.2995    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2995 r_free = 0.2995    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2995
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.1649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   9269  Z= 0.196
  Angle     :  0.632   9.522  12630  Z= 0.329
  Chirality :  0.048   0.149   1559
  Planarity :  0.005   0.043   1621
  Dihedral  :  4.837  27.791   1307
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 23.24 %
    Favored  : 72.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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 aren not related in a simple way.
  whole: -0.40 (0.25), residues: 1223
  helix:  1.47 (0.23), residues: 545
  sheet: -0.72 (0.38), residues: 176
  loop : -2.13 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 211 
 TYR   0.009   0.001   TYR D 259 
 PHE   0.013   0.002   PHE D  27 
 HIS   0.004   0.001   HIS D 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 9269)
  covalent geometry    : angle       0.63197 (12630)
  hydrogen bonds       : bond        0.06223 (  418)
  hydrogen bonds       : angle       4.32788 ( 1236)

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 70
  time to evaluate  : 0.368 
Fit side-chains
REVERT: B    7 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.7993 (mm)
REVERT: B   68 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.6300 (mtp180)
REVERT: B   74 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.6954 (tp30)
REVERT: B   77 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7166 (mp0)
REVERT: B  263 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7477 (t70)
REVERT: B  267 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7862 (mp0)
REVERT: B  293 ILE cc_start: 0.9277 (pt) cc_final: 0.9029 (pt)
REVERT: C   73 THR cc_start: 0.8726 (p) cc_final: 0.8519 (t)
REVERT: C  303 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.8041 (mp0)
REVERT: D    7 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.7984 (mm)
REVERT: D   51 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.7637 (tpt-90)
  outliers start: 38
  outliers final: 27
  residues processed: 101
  average time/residue: 0.0996
  time to fit residues: 14.3200
Evaluate side-chains
  105 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 69
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  159 ASP
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   50 ASP
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   68 ARG
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  230 SER
Chi-restraints excluded: chain B residue  263 ASP
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain B residue  302 GLU
Chi-restraints excluded: chain C residue  131 ASN
Chi-restraints excluded: chain C residue  230 SER
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain D residue    7 ILE
Chi-restraints excluded: chain D residue   51 ARG
Chi-restraints excluded: chain D residue   55 THR
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  153 LEU
Chi-restraints excluded: chain D residue  159 ASP
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  248 LYS
Chi-restraints excluded: chain D residue  275 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 39 optimal weight:    9.9990
   chunk 76 optimal weight:    2.9990
   chunk 83 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 108 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 4 optimal weight:    6.9990
   chunk 94 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9990
   chunk 103 optimal weight:    0.9980
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.118848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.096564 restraints weight = 27057.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 3.26
r_work: 0.3031 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3034
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3034
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9269  Z= 0.164
  Angle     :  0.603   8.861  12630  Z= 0.314
  Chirality :  0.047   0.139   1559
  Planarity :  0.005   0.043   1621
  Dihedral  :  4.778  27.637   1307
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 23.14 %
    Favored  : 73.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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 aren not related in a simple way.
  whole: -0.32 (0.25), residues: 1223
  helix:  1.57 (0.23), residues: 541
  sheet: -0.71 (0.38), residues: 176
  loop : -2.08 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  23 
 TYR   0.007   0.001   TYR D 261 
 PHE   0.012   0.001   PHE D  27 
 HIS   0.003   0.001   HIS D 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 9269)
  covalent geometry    : angle       0.60319 (12630)
  hydrogen bonds       : bond        0.05610 (  418)
  hydrogen bonds       : angle       4.23879 ( 1236)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2207.67 seconds
wall clock time: 38 minutes 32.20 seconds (2312.20 seconds total)