Starting phenix.real_space_refine
on Fri Nov 15 15:59:49 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jil_36317/11_2024/8jil_36317_neut.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jil_36317/11_2024/8jil_36317.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jil_36317/11_2024/8jil_36317.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jil_36317/11_2024/8jil_36317.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jil_36317/11_2024/8jil_36317_neut.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jil_36317/11_2024/8jil_36317_neut.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.011 sd=   0.078
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      69      5.16       5
     C    5765      2.51       5
     N    1535      2.21       5
     O    1659      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 9028
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2611
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "D"
      Number of atoms: 1796
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1796
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2364
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2364
          Classifications: {'peptide': 288}
          Link IDs: {'PTRANS': 9, 'TRANS': 278}
    Chain: "A"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'CLR': 1, 'NIO': 1}
          Classifications: {'undetermined': 2, 'water': 1}
          Link IDs: {None: 2}
  Time building chain proxies: 4.96, per 1000 atoms: 0.55
  Number of scatterers: 9028
  At special positions: 0
  Unit cell: (109.48, 135.24, 104.88, 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      69     16.00
     O    1659      8.00
     N    1535      7.00
     C    5765      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A  18 " - pdb=" SG  CYS A 183 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  19 " - pdb=" SG  CYS A 266 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 100 " - pdb=" SG  CYS A 177 " distance=2.03

  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: 2.42
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2134

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 13 sheets defined
      34.3% alpha, 21.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'B' and resid 1 through 25
      removed outlier: 3.614A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.518A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 23
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.525A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 11 through 27
    Processing helix  chain 'D' and resid 45 through 53
    Processing helix  chain 'D' and resid 211 through 216
    Processing helix  chain 'D' and resid 241 through 254
      removed outlier: 3.726A  pdb=" N   ALA D 245 " --> pdb=" O   ASN D 241 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 255 through 260
      removed outlier: 6.118A  pdb=" N   TRP D 258 " --> pdb=" O   ASN D 255 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   THR D 260 " --> pdb=" O   LYS D 257 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 270 through 281
      removed outlier: 3.945A  pdb=" N   GLU D 276 " --> pdb=" O   ASP D 272 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   LYS D 279 " --> pdb=" O   GLU D 275 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LYS D 280 " --> pdb=" O   GLU D 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 295 through 309
      removed outlier: 3.691A  pdb=" N   ALA D 299 " --> pdb=" O   THR D 295 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 329 through 351
      removed outlier: 3.816A  pdb=" N   GLN D 333 " --> pdb=" O   THR D 329 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL D 342 " --> pdb=" O   ALA D 338 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   CYS D 351 " --> pdb=" O   ASN D 347 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'A' and resid 25 through 55
      removed outlier: 3.749A  pdb=" N   VAL A  29 " --> pdb=" O   PHE A  25 " (cutoff:3.500A)
      Proline residue:  A  31  - end of helix
      removed outlier: 4.211A  pdb=" N   LEU A  43 " --> pdb=" O   ILE A  39 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ALA A  48 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 79
      removed outlier: 3.948A  pdb=" N   LEU A  66 " --> pdb=" O   SER A  62 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   ASN A  68 " --> pdb=" O   ILE A  64 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU A  69 " --> pdb=" O   PHE A  65 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ASP A  73 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   PHE A  74 " --> pdb=" O   ALA A  70 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU A  76 " --> pdb=" O   ALA A  72 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ILE A  78 " --> pdb=" O   PHE A  74 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   CYS A  79 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 89
      removed outlier: 3.782A  pdb=" N   LEU A  83 " --> pdb=" O   CYS A  79 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ARG A  89 " --> pdb=" O   ASP A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 114
      removed outlier: 4.251A  pdb=" N   PHE A 105 " --> pdb=" O   ARG A 101 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   MET A 106 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LEU A 107 " --> pdb=" O   MET A 103 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   ALA A 108 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ARG A 111 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLN A 112 " --> pdb=" O   ALA A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 120
      removed outlier: 3.622A  pdb=" N   VAL A 120 " --> pdb=" O   ILE A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 130
      removed outlier: 4.231A  pdb=" N   TYR A 126 " --> pdb=" O   ALA A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 139
      removed outlier: 4.144A  pdb=" N   ILE A 139 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 158
    Processing helix  chain 'A' and resid 159 through 163
    Processing helix  chain 'A' and resid 187 through 215
      removed outlier: 4.223A  pdb=" N   ALA A 191 " --> pdb=" O   GLN A 187 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   PHE A 197 " --> pdb=" O   PHE A 193 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   LEU A 199 " --> pdb=" O   LEU A 195 " (cutoff:3.500A)
      Proline residue:  A 200  - end of helix
      removed outlier: 4.390A  pdb=" N   PHE A 206 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ILE A 212 " --> pdb=" O   SER A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 261
      removed outlier: 3.740A  pdb=" N   LYS A 227 " --> pdb=" O   HIS A 223 " (cutoff:3.500A)
      Proline residue:  A 246  - end of helix
      removed outlier: 3.528A  pdb=" N   ARG A 251 " --> pdb=" O   SER A 247 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ILE A 252 " --> pdb=" O   VAL A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 270
    Processing helix  chain 'A' and resid 271 through 280
    Processing helix  chain 'A' and resid 281 through 283
      No H-bonds generated for 'chain 'A' and resid 281 through 283'
    Processing helix  chain 'A' and resid 284 through 290
      removed outlier: 3.550A  pdb=" N   MET A 288 " --> pdb=" O   TYR A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 295
    Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 52
      removed outlier: 6.555A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  49 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.860A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.098A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.857A  pdb=" N   THR B 102 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 5.928A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.685A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.524A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.099A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.563A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.634A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277
      removed outlier: 6.496A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 5.448A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 185 through 190
      removed outlier: 3.561A  pdb=" N   PHE D 189 " --> pdb=" O   PHE D 196 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   LYS D  35 " --> pdb=" O   ALA D 220 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   ILE D 222 " --> pdb=" O   LYS D  35 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   LEU D  37 " --> pdb=" O   ILE D 222 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   CYS D 224 " --> pdb=" O   LEU D  37 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   LEU D  39 " --> pdb=" O   CYS D 224 " (cutoff:3.500A)
      removed outlier: 8.869A  pdb=" N   ALA D 226 " --> pdb=" O   LEU D  39 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
      removed outlier: 7.235A  pdb=" N   GLY S  16 " --> pdb=" O   SER S  85 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   SER S  85 " --> pdb=" O   GLY S  16 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.080A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 146 through 148
      removed outlier: 3.642A  pdb=" N   GLU S 246 " --> pdb=" O   VAL S 147 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   THR S 243 " --> pdb=" O   TYR S 227 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   TYR S 227 " --> pdb=" O   THR S 243 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 155 through 160
    Processing sheet with id=AB4, first strand: chain 'A' and resid 11 through 13

    364 hydrogen bonds defined for protein.
    1017 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.42

  Time building geometry restraints manager: 2.79 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: 2903
        1.34 -     1.47: 2302
        1.47 -     1.60: 3920
        1.60 -     1.72: 0
        1.72 -     1.85: 100
  Bond restraints: 9225
  Sorted by residual:
  bond pdb=" CA  SER A 179 "
       pdb=" CB  SER A 179 "
    ideal  model  delta    sigma   weight residual
    1.537  1.480  0.057 1.38e-02 5.25e+03 1.70e+01
  bond pdb=" N   CYS A 183 "
       pdb=" CA  CYS A 183 "
    ideal  model  delta    sigma   weight residual
    1.453  1.496 -0.043 1.39e-02 5.18e+03 9.61e+00
  bond pdb=" N   PHE A 186 "
       pdb=" CA  PHE A 186 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.037 1.22e-02 6.72e+03 9.25e+00
  bond pdb=" N   ILE A  77 "
       pdb=" CA  ILE A  77 "
    ideal  model  delta    sigma   weight residual
    1.462  1.495 -0.033 1.18e-02 7.18e+03 7.87e+00
  bond pdb=" N   SER A 179 "
       pdb=" CA  SER A 179 "
    ideal  model  delta    sigma   weight residual
    1.454  1.491 -0.037 1.31e-02 5.83e+03 7.82e+00
  ... (remaining 9220 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.83: 12292
        2.83 -     5.67: 172
        5.67 -     8.50: 17
        8.50 -    11.34: 3
       11.34 -    14.17: 1
  Bond angle restraints: 12485
  Sorted by residual:
  angle pdb=" CB  MET S 230 "
        pdb=" CG  MET S 230 "
        pdb=" SD  MET S 230 "
      ideal   model   delta    sigma   weight residual
     112.70  126.87  -14.17 3.00e+00 1.11e-01 2.23e+01
  angle pdb=" N   SER A 178 "
        pdb=" CA  SER A 178 "
        pdb=" C   SER A 178 "
      ideal   model   delta    sigma   weight residual
     108.96  114.78   -5.82 1.49e+00 4.50e-01 1.53e+01
  angle pdb=" N   SER A 179 "
        pdb=" CA  SER A 179 "
        pdb=" C   SER A 179 "
      ideal   model   delta    sigma   weight residual
     114.31  109.31    5.00 1.29e+00 6.01e-01 1.50e+01
  angle pdb=" CA  MET C  21 "
        pdb=" CB  MET C  21 "
        pdb=" CG  MET C  21 "
      ideal   model   delta    sigma   weight residual
     114.10  121.68   -7.58 2.00e+00 2.50e-01 1.44e+01
  angle pdb=" C   CYS A 183 "
        pdb=" CA  CYS A 183 "
        pdb=" CB  CYS A 183 "
      ideal   model   delta    sigma   weight residual
     112.43  105.21    7.22 1.91e+00 2.74e-01 1.43e+01
  ... (remaining 12480 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.33: 4887
       16.33 -    32.67: 506
       32.67 -    49.00: 100
       49.00 -    65.34: 10
       65.34 -    81.67: 8
  Dihedral angle restraints: 5511
    sinusoidal: 2208
      harmonic: 3303
  Sorted by residual:
  dihedral pdb=" CA  PHE S 239 "
           pdb=" C   PHE S 239 "
           pdb=" N   GLY S 240 "
           pdb=" CA  GLY S 240 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.39   25.61     0      5.00e+00 4.00e-02 2.62e+01
  dihedral pdb=" CA  ASP A  14 "
           pdb=" C   ASP A  14 "
           pdb=" N   LYS A  15 "
           pdb=" CA  LYS A  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.94   23.06     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  GLU D   8 "
           pdb=" C   GLU D   8 "
           pdb=" N   ASP D   9 "
           pdb=" CA  ASP D   9 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.14   20.86     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 5508 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 837
       0.037 -    0.075: 371
       0.075 -    0.112: 146
       0.112 -    0.150: 39
       0.150 -    0.187: 10
  Chirality restraints: 1403
  Sorted by residual:
  chirality pdb=" CA  VAL S  37 "
            pdb=" N   VAL S  37 "
            pdb=" C   VAL S  37 "
            pdb=" CB  VAL S  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.76e-01
  chirality pdb=" CA  LEU A  76 "
            pdb=" N   LEU A  76 "
            pdb=" C   LEU A  76 "
            pdb=" CB  LEU A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.08e-01
  chirality pdb=" CA  CYS A 177 "
            pdb=" N   CYS A 177 "
            pdb=" C   CYS A 177 "
            pdb=" CB  CYS A 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.28e-01
  ... (remaining 1400 not shown)

  Planarity restraints: 1574
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 182 "   -0.015 2.00e-02 2.50e+03   2.93e-02 8.57e+00
        pdb=" C   ILE A 182 "    0.051 2.00e-02 2.50e+03
        pdb=" O   ILE A 182 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   CYS A 183 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  48 "   -0.045 5.00e-02 4.00e+02   6.91e-02 7.63e+00
        pdb=" N   PRO C  49 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO C  49 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO C  49 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP S  74 "    0.038 5.00e-02 4.00e+02   5.85e-02 5.48e+00
        pdb=" N   PRO S  75 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO S  75 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO S  75 "    0.033 5.00e-02 4.00e+02
  ... (remaining 1571 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1058
        2.75 -     3.29: 8595
        3.29 -     3.82: 14216
        3.82 -     4.36: 17102
        4.36 -     4.90: 30046
  Nonbonded interactions: 71017
  Sorted by model distance:
  nonbonded pdb=" O   ALA C  56 "
            pdb=" NH1 ARG C  62 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" NH1 ARG B  49 "
            pdb=" O   PHE C  61 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" O   ASP B 333 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" NH2 ARG B  22 "
            pdb=" O   THR B 221 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" OG  SER S  30 "
            pdb=" OD1 ASP S  74 "
     model   vdw
     2.279 3.040
  ... (remaining 71012 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     22.760
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6924
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      :  0.006   0.061   9225  Z= 0.362
  Angle     :  0.876  14.172  12485  Z= 0.502
  Chirality :  0.050   0.187   1403
  Planarity :  0.005   0.069   1574
  Dihedral  : 13.683  81.670   3365
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.41 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.24), residues: 1127
  helix: -0.21 (0.29), residues: 325
  sheet: -0.34 (0.30), residues: 273
  loop : -2.35 (0.24), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP B 169 
 HIS   0.010   0.002   HIS A 189 
 PHE   0.023   0.002   PHE A 105 
 TYR   0.022   0.002   TYR S  50 
 ARG   0.005   0.001   ARG A 251 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 1.040 
Fit side-chains
REVERT: A  167 MET cc_start: 0.5256 (tpt) cc_final: 0.5011 (tpp)
REVERT: A  217 GLN cc_start: 0.7802 (pp30) cc_final: 0.7594 (pp30)
  outliers start: 1
  outliers final: 1
  residues processed: 116
  average time/residue: 0.2869
  time to fit residues: 43.8755
Evaluate side-chains
  98 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   45 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 28 optimal weight:    0.3980
   chunk 57 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 53 optimal weight:    0.2980
   chunk 65 optimal weight:    4.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
C  18 GLN
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6896
moved from start:          0.1081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9225  Z= 0.217
  Angle     :  0.671  10.521  12485  Z= 0.342
  Chirality :  0.045   0.146   1403
  Planarity :  0.005   0.059   1574
  Dihedral  :  6.036  51.981   1300
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  6.92 %
    Favored  : 92.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.24), residues: 1127
  helix:  0.31 (0.29), residues: 335
  sheet: -0.22 (0.30), residues: 281
  loop : -2.26 (0.25), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 169 
 HIS   0.008   0.002   HIS A 184 
 PHE   0.018   0.002   PHE A  67 
 TYR   0.014   0.002   TYR B 105 
 ARG   0.003   0.000   ARG A  89 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 1.306 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 ARG cc_start: 0.7875 (ttp-170) cc_final: 0.7646 (mtm180)
REVERT: A  167 MET cc_start: 0.5063 (tpt) cc_final: 0.4808 (tpp)
  outliers start: 6
  outliers final: 1
  residues processed: 108
  average time/residue: 0.3027
  time to fit residues: 43.2389
Evaluate side-chains
  98 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   45 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 31 optimal weight:    0.1980
   chunk 84 optimal weight:    0.1980
   chunk 69 optimal weight:    0.4980
   chunk 28 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9990
   chunk 110 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   chunk 81 optimal weight:    0.0020
   chunk 100 optimal weight:    7.9990
   overall best weight:    0.3588

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
D 188 HIS
A 131 HIS
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6840
moved from start:          0.1591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.095   9225  Z= 0.162
  Angle     :  0.595  10.351  12485  Z= 0.304
  Chirality :  0.043   0.169   1403
  Planarity :  0.004   0.053   1574
  Dihedral  :  5.598  47.117   1300
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  9.66 %
    Favored  : 89.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.24), residues: 1127
  helix:  0.77 (0.30), residues: 340
  sheet: -0.11 (0.30), residues: 282
  loop : -2.09 (0.25), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 169 
 HIS   0.007   0.001   HIS A 133 
 PHE   0.012   0.001   PHE A 105 
 TYR   0.008   0.001   TYR S  95 
 ARG   0.005   0.000   ARG A 222 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
REVERT: D  227 LEU cc_start: 0.5149 (OUTLIER) cc_final: 0.4775 (pp)
REVERT: D  276 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6869 (mm-30)
REVERT: A  101 ARG cc_start: 0.7852 (ttp-170) cc_final: 0.7648 (mtm180)
  outliers start: 12
  outliers final: 4
  residues processed: 120
  average time/residue: 0.2616
  time to fit residues: 42.0550
Evaluate side-chains
  106 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  227 LEU
Chi-restraints excluded: chain D residue  276 GLU
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  278 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9980
   chunk 108 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B 110 ASN
B 175 GLN
B 268 ASN
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6879
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   9225  Z= 0.209
  Angle     :  0.610  10.077  12485  Z= 0.311
  Chirality :  0.044   0.198   1403
  Planarity :  0.004   0.052   1574
  Dihedral  :  5.653  48.197   1300
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 11.19 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.24), residues: 1127
  helix:  0.81 (0.30), residues: 339
  sheet:  0.01 (0.30), residues: 280
  loop : -2.02 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 169 
 HIS   0.006   0.001   HIS A 133 
 PHE   0.023   0.002   PHE S  29 
 TYR   0.015   0.001   TYR B 105 
 ARG   0.005   0.000   ARG A 222 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  227 LEU cc_start: 0.5200 (OUTLIER) cc_final: 0.4875 (pp)
REVERT: D  272 ASP cc_start: 0.5495 (m-30) cc_final: 0.4799 (m-30)
REVERT: D  276 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6872 (mm-30)
REVERT: A  103 MET cc_start: 0.6198 (ttt) cc_final: 0.5829 (ttt)
REVERT: A  167 MET cc_start: 0.5164 (tpp) cc_final: 0.4956 (tpp)
  outliers start: 16
  outliers final: 8
  residues processed: 116
  average time/residue: 0.2496
  time to fit residues: 39.1535
Evaluate side-chains
  110 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain D residue  227 LEU
Chi-restraints excluded: chain D residue  276 GLU
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  242 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 61 optimal weight:    8.9990
   chunk 1 optimal weight:    7.9990
   chunk 80 optimal weight:    5.9990
   chunk 44 optimal weight:    0.6980
   chunk 92 optimal weight:    5.9990
   chunk 74 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 55 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
B 175 GLN
A  45 ASN
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6989
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.064   9225  Z= 0.461
  Angle     :  0.789  11.825  12485  Z= 0.402
  Chirality :  0.051   0.206   1403
  Planarity :  0.005   0.053   1574
  Dihedral  :  6.431  60.285   1300
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 13.22 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.24), residues: 1127
  helix:  0.35 (0.29), residues: 339
  sheet: -0.32 (0.30), residues: 277
  loop : -2.16 (0.24), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 169 
 HIS   0.015   0.002   HIS A 189 
 PHE   0.024   0.003   PHE S  29 
 TYR   0.025   0.003   TYR S  50 
 ARG   0.006   0.001   ARG A 222 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
REVERT: D  276 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6399 (mp0)
REVERT: A  103 MET cc_start: 0.6395 (ttt) cc_final: 0.5928 (ttt)
REVERT: A  167 MET cc_start: 0.5055 (tpp) cc_final: 0.4794 (tpp)
  outliers start: 19
  outliers final: 11
  residues processed: 117
  average time/residue: 0.2289
  time to fit residues: 36.8575
Evaluate side-chains
  110 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain D residue  276 GLU
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  290 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 97 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 63 optimal weight:    7.9990
   chunk 26 optimal weight:    0.0770
   chunk 108 optimal weight:    2.9990
   chunk 89 optimal weight:    0.0570
   chunk 50 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9980
   chunk 35 optimal weight:    8.9990
   chunk 56 optimal weight:    1.9990
   chunk 104 optimal weight:    0.0070
   overall best weight:    0.4074

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6889
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9225  Z= 0.169
  Angle     :  0.600  10.619  12485  Z= 0.307
  Chirality :  0.043   0.167   1403
  Planarity :  0.004   0.057   1574
  Dihedral  :  5.697  52.257   1300
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 15.46 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.24), residues: 1127
  helix:  0.83 (0.30), residues: 340
  sheet: -0.14 (0.29), residues: 285
  loop : -2.04 (0.25), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.009   0.001   HIS A 133 
 PHE   0.018   0.001   PHE S  29 
 TYR   0.010   0.001   TYR B 105 
 ARG   0.009   0.000   ARG S  67 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 1.038 
Fit side-chains
REVERT: D  272 ASP cc_start: 0.5478 (m-30) cc_final: 0.4819 (m-30)
REVERT: D  276 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6798 (mm-30)
REVERT: A  103 MET cc_start: 0.5974 (ttt) cc_final: 0.5767 (ttt)
REVERT: A  167 MET cc_start: 0.5025 (tpp) cc_final: 0.4791 (tpp)
  outliers start: 14
  outliers final: 6
  residues processed: 116
  average time/residue: 0.2474
  time to fit residues: 38.9706
Evaluate side-chains
  110 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  276 GLU
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  182 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 61 optimal weight:   10.0000
   chunk 79 optimal weight:    6.9990
   chunk 91 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   chunk 107 optimal weight:    0.4980
   chunk 67 optimal weight:    0.0040
   chunk 65 optimal weight:    0.7980
   chunk 49 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6878
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9225  Z= 0.175
  Angle     :  0.581  10.284  12485  Z= 0.297
  Chirality :  0.043   0.152   1403
  Planarity :  0.004   0.055   1574
  Dihedral  :  5.503  49.768   1300
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 15.77 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.24), residues: 1127
  helix:  1.00 (0.30), residues: 339
  sheet: -0.08 (0.29), residues: 286
  loop : -1.95 (0.25), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.008   0.001   HIS A 133 
 PHE   0.018   0.001   PHE S  29 
 TYR   0.020   0.001   TYR S  95 
 ARG   0.004   0.000   ARG A 222 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
REVERT: D  272 ASP cc_start: 0.5429 (m-30) cc_final: 0.4814 (m-30)
REVERT: D  276 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6811 (mm-30)
REVERT: S    6 GLU cc_start: 0.6356 (pt0) cc_final: 0.6084 (pt0)
REVERT: S  118 THR cc_start: 0.8114 (m) cc_final: 0.7725 (p)
REVERT: A  103 MET cc_start: 0.5921 (ttt) cc_final: 0.5697 (ttt)
  outliers start: 12
  outliers final: 8
  residues processed: 117
  average time/residue: 0.2530
  time to fit residues: 39.8410
Evaluate side-chains
  113 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain D residue  276 GLU
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  290 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 73 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 84 optimal weight:    5.9990
   chunk 98 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6912
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   9225  Z= 0.237
  Angle     :  0.618  10.216  12485  Z= 0.315
  Chirality :  0.044   0.160   1403
  Planarity :  0.004   0.053   1574
  Dihedral  :  5.615  45.121   1300
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 15.97 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.24), residues: 1127
  helix:  0.92 (0.30), residues: 339
  sheet: -0.13 (0.29), residues: 280
  loop : -1.98 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.007   0.001   HIS A 133 
 PHE   0.018   0.002   PHE S  29 
 TYR   0.015   0.002   TYR S  95 
 ARG   0.003   0.000   ARG A 222 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
REVERT: D  272 ASP cc_start: 0.5518 (m-30) cc_final: 0.4844 (m-30)
REVERT: D  276 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6832 (mm-30)
REVERT: S    6 GLU cc_start: 0.6408 (pt0) cc_final: 0.6188 (pt0)
REVERT: A   40 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.6649 (m-10)
  outliers start: 15
  outliers final: 11
  residues processed: 114
  average time/residue: 0.2554
  time to fit residues: 39.0634
Evaluate side-chains
  114 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain D residue  227 LEU
Chi-restraints excluded: chain D residue  276 GLU
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  290 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.8980
   chunk 100 optimal weight:    0.2980
   chunk 103 optimal weight:    0.6980
   chunk 60 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 90 optimal weight:    0.8980
   chunk 95 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6879
moved from start:          0.2227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9225  Z= 0.177
  Angle     :  0.581  10.494  12485  Z= 0.298
  Chirality :  0.043   0.149   1403
  Planarity :  0.004   0.053   1574
  Dihedral  :  5.399  42.090   1300
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.87 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.25), residues: 1127
  helix:  1.05 (0.30), residues: 339
  sheet: -0.05 (0.30), residues: 271
  loop : -1.88 (0.25), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.008   0.001   HIS A 184 
 PHE   0.017   0.001   PHE S  29 
 TYR   0.018   0.001   TYR S  95 
 ARG   0.004   0.000   ARG A 222 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.947 
Fit side-chains
REVERT: D  272 ASP cc_start: 0.5570 (m-30) cc_final: 0.4962 (m-30)
REVERT: D  276 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6737 (mm-30)
REVERT: S    6 GLU cc_start: 0.6359 (pt0) cc_final: 0.6146 (pt0)
REVERT: S  233 LEU cc_start: 0.5245 (tp) cc_final: 0.5022 (tp)
  outliers start: 17
  outliers final: 10
  residues processed: 114
  average time/residue: 0.2490
  time to fit residues: 38.3195
Evaluate side-chains
  112 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain D residue  227 LEU
Chi-restraints excluded: chain D residue  276 GLU
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  290 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 73 optimal weight:    0.5980
   chunk 111 optimal weight:    0.6980
   chunk 102 optimal weight:    0.9990
   chunk 88 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9980
   chunk 94 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6876
moved from start:          0.2309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9225  Z= 0.181
  Angle     :  0.585  10.348  12485  Z= 0.300
  Chirality :  0.043   0.143   1403
  Planarity :  0.004   0.053   1574
  Dihedral  :  5.349  40.962   1300
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 16.17 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.25), residues: 1127
  helix:  1.08 (0.30), residues: 339
  sheet: -0.04 (0.30), residues: 271
  loop : -1.85 (0.25), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.009   0.001   HIS A 184 
 PHE   0.017   0.001   PHE S  29 
 TYR   0.017   0.001   TYR S  95 
 ARG   0.009   0.000   ARG A 222 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.916 
Fit side-chains
REVERT: B  176 GLN cc_start: 0.8588 (mt0) cc_final: 0.8382 (mt0)
REVERT: D  276 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6734 (mm-30)
REVERT: S    6 GLU cc_start: 0.6344 (pt0) cc_final: 0.6140 (pt0)
  outliers start: 13
  outliers final: 10
  residues processed: 113
  average time/residue: 0.2601
  time to fit residues: 39.6599
Evaluate side-chains
  112 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain D residue  227 LEU
Chi-restraints excluded: chain D residue  276 GLU
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  290 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 81 optimal weight:    9.9990
   chunk 13 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9990
   chunk 37 optimal weight:    6.9990
   chunk 91 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 78 optimal weight:    0.1980
   chunk 5 optimal weight:    4.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.146780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.127413 restraints weight = 15087.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.126731 restraints weight = 21053.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.127033 restraints weight = 18705.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6854
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9225  Z= 0.208
  Angle     :  0.611  10.288  12485  Z= 0.314
  Chirality :  0.044   0.224   1403
  Planarity :  0.004   0.052   1574
  Dihedral  :  5.450  42.346   1300
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 16.48 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.24), residues: 1127
  helix:  1.03 (0.30), residues: 339
  sheet: -0.08 (0.30), residues: 275
  loop : -1.84 (0.25), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.017   0.001   HIS A 184 
 PHE   0.017   0.002   PHE S  29 
 TYR   0.015   0.001   TYR S  95 
 ARG   0.009   0.000   ARG A 222 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1888.97 seconds
wall clock time: 35 minutes 33.36 seconds (2133.36 seconds total)