Starting phenix.real_space_refine
on Wed Feb 12 17:44:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7cfm_30344/02_2025/7cfm_30344.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7cfm_30344/02_2025/7cfm_30344.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7cfm_30344/02_2025/7cfm_30344.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7cfm_30344/02_2025/7cfm_30344.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7cfm_30344/02_2025/7cfm_30344.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7cfm_30344/02_2025/7cfm_30344.cif"
  }
  resolution = 3.0
  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=  -0.000 sd=   0.011
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      46      5.16       5
     C    5140      2.51       5
     N    1419      2.21       5
     O    1476      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8081
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1897
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 229, 1886
          Classifications: {'peptide': 229}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 222}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
      Conformer: "C"
        Number of residues, atoms: 229, 1886
          Classifications: {'peptide': 229}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 222}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
          bond proxies already assigned to first conformer: 1910
    Chain: "B"
      Number of atoms: 2604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2604
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 12
    Chain: "G"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 438
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "N"
      Number of atoms: 965
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 965
          Classifications: {'peptide': 127}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "R"
      Number of atoms: 2063
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2063
          Classifications: {'peptide': 273}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 21, 'TRANS': 251}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "R"
      Number of atoms: 114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 114
          Unusual residues: {'CLR': 3, 'FWX': 1}
          Classifications: {'undetermined': 4, 'water': 1}
          Link IDs: {None: 4}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG A 380 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2CARG A 380 " occ=0.62
  Time building chain proxies: 5.52, per 1000 atoms: 0.68
  Number of scatterers: 8081
  At special positions: 0
  Unit cell: (79.092, 113.568, 122.694, 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      46     16.00
     O    1476      8.00
     N    1419      7.00
     C    5140      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  85 " - pdb=" SG  CYS R 155 " 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: 2.13
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1916

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      41.2% alpha, 18.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 3.889A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 59
    Processing helix  chain 'A' and resid 233 through 237
      removed outlier: 3.610A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 233 through 237'
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.922A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ALA A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.128A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.889A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 2 through 26
      removed outlier: 3.667A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 6 through 24
      removed outlier: 4.097A  pdb=" N   ALA G  10 " --> pdb=" O   THR G   6 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.510A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 28 through 32'
    Processing helix  chain 'R' and resid 21 through 42
      removed outlier: 4.095A  pdb=" N   ASP R  42 " --> pdb=" O   GLY R  38 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 48 through 68
      removed outlier: 3.519A  pdb=" N   CYS R  52 " --> pdb=" O   PRO R  48 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 81 through 116
      removed outlier: 3.921A  pdb=" N   LEU R  87 " --> pdb=" O   TRP R  83 " (cutoff:3.500A)
      Proline residue:  R  92  - end of helix
    Processing helix  chain 'R' and resid 123 through 145
      removed outlier: 3.776A  pdb=" N   ALA R 127 " --> pdb=" O   SER R 123 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLY R 134 " --> pdb=" O   LEU R 130 " (cutoff:3.500A)
      Proline residue:  R 135  - end of helix
      Proline residue:  R 142  - end of helix
      removed outlier: 3.749A  pdb=" N   GLY R 145 " --> pdb=" O   LEU R 141 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 156 through 161
    Processing helix  chain 'R' and resid 162 through 173
    Processing helix  chain 'R' and resid 173 through 207
      removed outlier: 3.522A  pdb=" N   VAL R 178 " --> pdb=" O   LEU R 174 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   LEU R 202 " --> pdb=" O   ASP R 198 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 212 through 252
      removed outlier: 3.730A  pdb=" N   ALA R 217 " --> pdb=" O   ALA R 213 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLY R 238 " --> pdb=" O   GLY R 234 " (cutoff:3.500A)
      Proline residue:  R 239  - end of helix
      removed outlier: 3.675A  pdb=" N   GLU R 252 " --> pdb=" O   VAL R 248 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 262 through 284
      Proline residue:  R 277  - end of helix
      removed outlier: 3.548A  pdb=" N   GLY R 283 " --> pdb=" O   ALA R 279 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ASP R 284 " --> pdb=" O   MET R 280 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 285 through 289
      removed outlier: 3.561A  pdb=" N   THR R 288 " --> pdb=" O   GLN R 285 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ALA R 289 " --> pdb=" O   ARG R 286 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 285 through 289'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213
      removed outlier: 9.779A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.644A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.344A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.702A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.580A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.082A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.223A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.672A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ASN B 125 " --> pdb=" O   ARG B 134 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151
      removed outlier: 4.103A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.529A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.419A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278
      removed outlier: 3.700A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.509A  pdb=" N   SER N  25 " --> pdb=" O   GLN N   3 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLN N   5 " --> pdb=" O   ALA N  23 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU N  81 " --> pdb=" O   LEU N  20 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 6.660A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    380 hydrogen bonds defined for protein.
    1117 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: 2.33

  Time building geometry restraints manager: 2.45 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: 2594
        1.34 -     1.46: 1957
        1.46 -     1.59: 3645
        1.59 -     1.71: 0
        1.71 -     1.84: 63
  Bond restraints: 8259
  Sorted by residual:
  bond pdb=" C04 FWX R 401 "
       pdb=" N03 FWX R 401 "
    ideal  model  delta    sigma   weight residual
    1.343  1.423 -0.080 2.00e-02 2.50e+03 1.61e+01
  bond pdb=" C12 FWX R 401 "
       pdb=" N09 FWX R 401 "
    ideal  model  delta    sigma   weight residual
    1.351  1.425 -0.074 2.00e-02 2.50e+03 1.37e+01
  bond pdb=" C04 FWX R 401 "
       pdb=" N26 FWX R 401 "
    ideal  model  delta    sigma   weight residual
    1.329  1.402 -0.073 2.00e-02 2.50e+03 1.34e+01
  bond pdb=" C   LYS N  87 "
       pdb=" N   PRO N  88 "
    ideal  model  delta    sigma   weight residual
    1.337  1.365 -0.028 9.80e-03 1.04e+04 8.35e+00
  bond pdb=" C06 FWX R 401 "
       pdb=" N05 FWX R 401 "
    ideal  model  delta    sigma   weight residual
    1.319  1.368 -0.049 2.00e-02 2.50e+03 5.94e+00
  ... (remaining 8254 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 10723
        2.09 -     4.18: 421
        4.18 -     6.27: 63
        6.27 -     8.36: 19
        8.36 -    10.45: 6
  Bond angle restraints: 11232
  Sorted by residual:
  angle pdb=" C   LYS B 127 "
        pdb=" N   THR B 128 "
        pdb=" CA  THR B 128 "
      ideal   model   delta    sigma   weight residual
     122.46  128.54   -6.08 1.41e+00 5.03e-01 1.86e+01
  angle pdb=" N   LEU R  45 "
        pdb=" CA  LEU R  45 "
        pdb=" C   LEU R  45 "
      ideal   model   delta    sigma   weight residual
     111.36  115.87   -4.51 1.09e+00 8.42e-01 1.71e+01
  angle pdb=" N   GLY A  47 "
        pdb=" CA  GLY A  47 "
        pdb=" C   GLY A  47 "
      ideal   model   delta    sigma   weight residual
     113.18  104.68    8.50 2.37e+00 1.78e-01 1.29e+01
  angle pdb=" C   PRO R 259 "
        pdb=" N   GLY R 260 "
        pdb=" CA  GLY R 260 "
      ideal   model   delta    sigma   weight residual
     121.41  128.28   -6.87 1.96e+00 2.60e-01 1.23e+01
  angle pdb=" CB  MET B 262 "
        pdb=" CG  MET B 262 "
        pdb=" SD  MET B 262 "
      ideal   model   delta    sigma   weight residual
     112.70  123.11  -10.41 3.00e+00 1.11e-01 1.20e+01
  ... (remaining 11227 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.38: 4798
       17.38 -    34.77: 210
       34.77 -    52.15: 39
       52.15 -    69.53: 9
       69.53 -    86.92: 11
  Dihedral angle restraints: 5067
    sinusoidal: 2096
      harmonic: 2971
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -7.94  -78.06     1      1.00e+01 1.00e-02 7.61e+01
  dihedral pdb=" CA  LYS B 301 "
           pdb=" C   LYS B 301 "
           pdb=" N   ALA B 302 "
           pdb=" CA  ALA B 302 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.55   27.45     0      5.00e+00 4.00e-02 3.01e+01
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -127.69   41.69     1      1.00e+01 1.00e-02 2.43e+01
  ... (remaining 5064 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 1102
       0.092 -    0.185: 148
       0.185 -    0.277: 13
       0.277 -    0.369: 1
       0.369 -    0.462: 1
  Chirality restraints: 1265
  Sorted by residual:
  chirality pdb=" C20 CLR R 402 "
            pdb=" C17 CLR R 402 "
            pdb=" C21 CLR R 402 "
            pdb=" C22 CLR R 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.59    2.13    0.46 2.00e-01 2.50e+01 5.33e+00
  chirality pdb=" C17 CLR R 402 "
            pdb=" C13 CLR R 402 "
            pdb=" C16 CLR R 402 "
            pdb=" C20 CLR R 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.25    0.30 2.00e-01 2.50e+01 2.32e+00
  chirality pdb=" CB  THR N  28 "
            pdb=" CA  THR N  28 "
            pdb=" OG1 THR N  28 "
            pdb=" CG2 THR N  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.29e+00
  ... (remaining 1262 not shown)

  Planarity restraints: 1428
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.040 5.00e-02 4.00e+02   5.99e-02 5.73e+00
        pdb=" N   PRO B 236 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 281 "   -0.021 2.00e-02 2.50e+03   1.35e-02 4.58e+00
        pdb=" CG  TRP A 281 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 281 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 281 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 281 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 281 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 281 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 281 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 281 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 281 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 331 "    0.034 5.00e-02 4.00e+02   5.21e-02 4.34e+00
        pdb=" N   PRO A 332 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 332 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 332 "    0.029 5.00e-02 4.00e+02
  ... (remaining 1425 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 37
        2.57 -     3.15: 5964
        3.15 -     3.74: 12202
        3.74 -     4.32: 16650
        4.32 -     4.90: 28524
  Nonbonded interactions: 63377
  Sorted by model distance:
  nonbonded pdb=" O   ASN A  54 "
            pdb=" CD  LYS A  58 "
     model   vdw
     1.988 3.440
  nonbonded pdb=" OH  TYR R 167 "
            pdb=" OE2 GLU R 252 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   ASP N  90 "
            pdb=" OH  TYR N  94 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   ARG N  98 "
            pdb=" OH  TYR N 115 "
     model   vdw
     2.322 3.040
  ... (remaining 63372 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=0.38 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:             0.430
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.020
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  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:11.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
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   0.080   8259  Z= 0.389
  Angle     :  0.989  10.451  11232  Z= 0.517
  Chirality :  0.062   0.462   1265
  Planarity :  0.007   0.060   1428
  Dihedral  : 11.281  86.917   3142
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  4.17 %
    Favored  : 95.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.23 (0.22), residues: 1016
  helix: -1.26 (0.20), residues: 393
  sheet: -0.89 (0.32), residues: 228
  loop : -1.89 (0.26), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP A 281 
 HIS   0.011   0.003   HIS B  54 
 PHE   0.020   0.003   PHE A 212 
 TYR   0.022   0.003   TYR A 339 
 ARG   0.013   0.001   ARG B 251 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 187
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  217 MET cc_start: 0.7492 (ptt) cc_final: 0.7046 (pp-130)
REVERT: B  228 ASP cc_start: 0.7736 (p0) cc_final: 0.7300 (p0)
REVERT: B  270 ILE cc_start: 0.8285 (pp) cc_final: 0.7912 (pp)
REVERT: G   21 MET cc_start: 0.7609 (tpt) cc_final: 0.7066 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 188
  average time/residue: 1.2559
  time to fit residues: 249.4602
Evaluate side-chains
  105 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 42 optimal weight:    0.4980
   chunk 25 optimal weight:    0.3980
   chunk 51 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 78 optimal weight:    0.7980
   chunk 30 optimal weight:    0.2980
   chunk 47 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
A 294 GLN
B 230 ASN
N  39 GLN
N  77 ASN
R 102 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.161565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.118463 restraints weight = 18269.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 3.65
r_work: 0.3191 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3148
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3148
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8259  Z= 0.172
  Angle     :  0.604   8.411  11232  Z= 0.303
  Chirality :  0.043   0.174   1265
  Planarity :  0.005   0.051   1428
  Dihedral  :  7.569  86.081   1332
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 11.79 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.54 (0.24), residues: 1016
  helix:  0.85 (0.24), residues: 393
  sheet: -0.58 (0.33), residues: 230
  loop : -1.40 (0.27), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 281 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.014   0.001   PHE N 108 
 TYR   0.019   0.001   TYR A 339 
 ARG   0.007   0.001   ARG A 228 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.7072 (ptp90)
REVERT: A  378 ASP cc_start: 0.7625 (m-30) cc_final: 0.7404 (m-30)
REVERT: B   14 LEU cc_start: 0.7879 (mt) cc_final: 0.7434 (mp)
REVERT: B  212 ASP cc_start: 0.8157 (t70) cc_final: 0.7758 (t70)
REVERT: B  217 MET cc_start: 0.8108 (ptt) cc_final: 0.7422 (pmt)
REVERT: B  270 ILE cc_start: 0.8242 (pp) cc_final: 0.7842 (pp)
REVERT: B  280 LYS cc_start: 0.8693 (tttm) cc_final: 0.8410 (ttpt)
REVERT: G   21 MET cc_start: 0.7586 (tpt) cc_final: 0.6946 (mmm)
REVERT: R   27 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6961 (tt)
  outliers start: 26
  outliers final: 8
  residues processed: 148
  average time/residue: 1.1079
  time to fit residues: 175.3565
Evaluate side-chains
  121 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  317 ARG
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue   27 LEU
Chi-restraints excluded: chain R residue  149 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 87 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0770
   chunk 67 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 79 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.7740

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A 278 ASN
A 292 ASN
N  39 GLN
N  77 ASN
R 119 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.160805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.117193 restraints weight = 21614.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 4.12
r_work: 0.3144 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3112
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3112 r_free = 0.3112    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3112 r_free = 0.3112    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3112
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8259  Z= 0.173
  Angle     :  0.563   8.549  11232  Z= 0.278
  Chirality :  0.043   0.185   1265
  Planarity :  0.004   0.050   1428
  Dihedral  :  7.123  85.921   1332
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 14.17 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.24 (0.26), residues: 1016
  helix:  1.79 (0.26), residues: 392
  sheet: -0.32 (0.35), residues: 222
  loop : -1.19 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 281 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.015   0.001   PHE N 108 
 TYR   0.020   0.001   TYR A 339 
 ARG   0.009   0.001   ARG R  79 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 112
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8502 (mttp)
REVERT: A  317 ARG cc_start: 0.7317 (ptp-110) cc_final: 0.7071 (ptp90)
REVERT: A  392 GLU cc_start: 0.8377 (tp30) cc_final: 0.8014 (mm-30)
REVERT: B  212 ASP cc_start: 0.8096 (t70) cc_final: 0.7652 (t70)
REVERT: B  217 MET cc_start: 0.8225 (ptt) cc_final: 0.7472 (pmt)
REVERT: B  226 GLU cc_start: 0.8351 (pt0) cc_final: 0.7825 (pt0)
REVERT: B  262 MET cc_start: 0.8528 (ttp) cc_final: 0.8312 (ptm)
REVERT: B  270 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7871 (pp)
REVERT: B  280 LYS cc_start: 0.8735 (tttm) cc_final: 0.8447 (ttpt)
REVERT: G   21 MET cc_start: 0.7646 (tpt) cc_final: 0.7103 (mmm)
REVERT: R   27 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6974 (mp)
REVERT: R  252 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8507 (mm-30)
  outliers start: 28
  outliers final: 11
  residues processed: 130
  average time/residue: 1.0158
  time to fit residues: 141.9513
Evaluate side-chains
  123 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain B residue   16 ASN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue   27 LEU
Chi-restraints excluded: chain R residue   33 LEU
Chi-restraints excluded: chain R residue  149 TRP
Chi-restraints excluded: chain R residue  231 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 62 optimal weight:    0.0370
   chunk 2 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 61 optimal weight:   10.0000
   chunk 78 optimal weight:    4.9990
   chunk 85 optimal weight:    7.9990
   chunk 81 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 68 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    1.4064

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

Flipped N/Q/H residues before XYZ refinement:
N  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.155094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.110238 restraints weight = 17818.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 3.28
r_work: 0.3092 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3071
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3071
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8259  Z= 0.239
  Angle     :  0.580   8.750  11232  Z= 0.289
  Chirality :  0.044   0.200   1265
  Planarity :  0.004   0.040   1428
  Dihedral  :  6.949  88.302   1332
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 14.40 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.52 (0.26), residues: 1016
  helix:  2.04 (0.26), residues: 392
  sheet: -0.08 (0.35), residues: 223
  loop : -1.12 (0.29), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 281 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.023   0.002   PHE N 108 
 TYR   0.024   0.001   TYR A 339 
 ARG   0.008   0.001   ARG B  19 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 113
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8560 (mttp)
REVERT: A  392 GLU cc_start: 0.8346 (tp30) cc_final: 0.8016 (mm-30)
REVERT: B   96 ARG cc_start: 0.7776 (ttt180) cc_final: 0.7505 (ttm110)
REVERT: B  212 ASP cc_start: 0.8213 (t70) cc_final: 0.7648 (t70)
REVERT: B  217 MET cc_start: 0.8220 (ptt) cc_final: 0.7501 (ppp)
REVERT: B  226 GLU cc_start: 0.8342 (pt0) cc_final: 0.7807 (pt0)
REVERT: B  270 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7873 (pp)
REVERT: B  280 LYS cc_start: 0.8722 (tttm) cc_final: 0.8428 (ttpt)
REVERT: G   21 MET cc_start: 0.7606 (tpt) cc_final: 0.7035 (mmm)
REVERT: R   27 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6799 (mp)
REVERT: R   97 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7486 (mt)
REVERT: R  154 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.7971 (m110)
REVERT: R  252 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8426 (mm-30)
  outliers start: 36
  outliers final: 13
  residues processed: 136
  average time/residue: 1.0243
  time to fit residues: 149.5336
Evaluate side-chains
  123 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   85 SER
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   27 LEU
Chi-restraints excluded: chain R residue   33 LEU
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  149 TRP
Chi-restraints excluded: chain R residue  154 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 51 optimal weight:    4.9990
   chunk 62 optimal weight:    0.0670
   chunk 93 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 64 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 95 optimal weight:    0.6980
   chunk 90 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
B  35 ASN
N  39 GLN
N  77 ASN
R 154 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.157917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.120264 restraints weight = 15802.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 3.76
r_work: 0.3148 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3108
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3108 r_free = 0.3108    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3108 r_free = 0.3108    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3108
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8259  Z= 0.156
  Angle     :  0.530  10.404  11232  Z= 0.261
  Chirality :  0.042   0.195   1265
  Planarity :  0.004   0.041   1428
  Dihedral  :  6.748  89.419   1332
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 16.07 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.88 (0.27), residues: 1016
  helix:  2.36 (0.26), residues: 394
  sheet:  0.08 (0.36), residues: 217
  loop : -0.92 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 281 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.010   0.001   PHE N 108 
 TYR   0.018   0.001   TYR A 339 
 ARG   0.010   0.000   ARG B  19 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8606 (mttp)
REVERT: A  392 GLU cc_start: 0.8326 (tp30) cc_final: 0.7888 (mm-30)
REVERT: B   14 LEU cc_start: 0.7935 (mt) cc_final: 0.7498 (mp)
REVERT: B   78 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8174 (mmtm)
REVERT: B  212 ASP cc_start: 0.8227 (t70) cc_final: 0.7640 (t70)
REVERT: B  217 MET cc_start: 0.8139 (ptt) cc_final: 0.7513 (pmt)
REVERT: B  226 GLU cc_start: 0.8342 (pt0) cc_final: 0.7775 (pt0)
REVERT: B  228 ASP cc_start: 0.8338 (p0) cc_final: 0.7975 (p0)
REVERT: B  270 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7974 (pp)
REVERT: B  280 LYS cc_start: 0.8736 (tttm) cc_final: 0.8507 (ttpt)
REVERT: G   21 MET cc_start: 0.7418 (tpt) cc_final: 0.6910 (mmm)
REVERT: N   60 TYR cc_start: 0.9024 (m-80) cc_final: 0.8668 (m-80)
REVERT: R  154 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.7938 (m-40)
REVERT: R  252 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8453 (mm-30)
  outliers start: 26
  outliers final: 11
  residues processed: 125
  average time/residue: 1.0478
  time to fit residues: 141.0443
Evaluate side-chains
  122 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain B residue   16 ASN
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain R residue   33 LEU
Chi-restraints excluded: chain R residue  149 TRP
Chi-restraints excluded: chain R residue  154 ASN
Chi-restraints excluded: chain R residue  231 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 95 optimal weight:    0.8980
   chunk 66 optimal weight:    0.4980
   chunk 10 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0670
   chunk 16 optimal weight:    8.9990
   chunk 48 optimal weight:    0.4980
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
N  77 ASN
** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.158133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.113870 restraints weight = 25154.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 4.44
r_work: 0.3121 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3080
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3080
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.2797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8259  Z= 0.148
  Angle     :  0.527   9.951  11232  Z= 0.258
  Chirality :  0.042   0.194   1265
  Planarity :  0.004   0.045   1428
  Dihedral  :  6.668  88.531   1332
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 16.90 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.05 (0.27), residues: 1016
  helix:  2.48 (0.26), residues: 394
  sheet:  0.15 (0.36), residues: 217
  loop : -0.79 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 281 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.011   0.001   PHE N 108 
 TYR   0.017   0.001   TYR A 339 
 ARG   0.010   0.000   ARG B  19 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8529 (mtmt)
REVERT: A  392 GLU cc_start: 0.8341 (tp30) cc_final: 0.7921 (mm-30)
REVERT: B   14 LEU cc_start: 0.7824 (mt) cc_final: 0.7379 (mp)
REVERT: B   78 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8049 (mmtm)
REVERT: B  212 ASP cc_start: 0.8110 (t70) cc_final: 0.7464 (t70)
REVERT: B  217 MET cc_start: 0.8094 (ptt) cc_final: 0.7328 (pmt)
REVERT: B  226 GLU cc_start: 0.8415 (pt0) cc_final: 0.7862 (pt0)
REVERT: B  228 ASP cc_start: 0.8369 (p0) cc_final: 0.7987 (p0)
REVERT: B  270 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7894 (pp)
REVERT: B  280 LYS cc_start: 0.8596 (tttm) cc_final: 0.8375 (ttpt)
REVERT: G   21 MET cc_start: 0.7360 (tpt) cc_final: 0.6904 (mmm)
REVERT: R   97 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7376 (mt)
REVERT: R  154 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7971 (m110)
REVERT: R  252 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8431 (mm-30)
  outliers start: 22
  outliers final: 12
  residues processed: 125
  average time/residue: 1.0421
  time to fit residues: 141.0210
Evaluate side-chains
  123 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain B residue   16 ASN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain R residue   33 LEU
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  149 TRP
Chi-restraints excluded: chain R residue  154 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0670
   chunk 80 optimal weight:    0.7980
   chunk 16 optimal weight:    8.9990
   chunk 47 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 52 optimal weight:    8.9990
   chunk 50 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 88 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
N  77 ASN
R  32 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.159023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.113624 restraints weight = 18297.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 3.35
r_work: 0.3151 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3107
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3107
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.2902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8259  Z= 0.150
  Angle     :  0.508   7.309  11232  Z= 0.252
  Chirality :  0.041   0.194   1265
  Planarity :  0.004   0.046   1428
  Dihedral  :  6.586  85.602   1332
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 16.79 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.21 (0.27), residues: 1016
  helix:  2.59 (0.26), residues: 397
  sheet:  0.20 (0.36), residues: 222
  loop : -0.70 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 281 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.012   0.001   PHE N 108 
 TYR   0.018   0.001   TYR A 339 
 ARG   0.010   0.000   ARG B  19 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8524 (mtmt)
REVERT: B   14 LEU cc_start: 0.7890 (mt) cc_final: 0.7437 (mp)
REVERT: B   78 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8103 (mmtm)
REVERT: B  212 ASP cc_start: 0.8077 (t70) cc_final: 0.7547 (t70)
REVERT: B  217 MET cc_start: 0.8129 (ptt) cc_final: 0.7746 (pmm)
REVERT: B  226 GLU cc_start: 0.8342 (pt0) cc_final: 0.7838 (pt0)
REVERT: B  228 ASP cc_start: 0.8395 (p0) cc_final: 0.8052 (p0)
REVERT: B  270 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7912 (pp)
REVERT: B  280 LYS cc_start: 0.8664 (tttm) cc_final: 0.8376 (ttpt)
REVERT: G   21 MET cc_start: 0.7404 (tpt) cc_final: 0.6865 (mmm)
REVERT: N   60 TYR cc_start: 0.9026 (m-80) cc_final: 0.8694 (m-80)
REVERT: R   27 LEU cc_start: 0.7036 (mp) cc_final: 0.6759 (tt)
REVERT: R   97 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7465 (mt)
  outliers start: 26
  outliers final: 15
  residues processed: 126
  average time/residue: 0.9873
  time to fit residues: 133.7379
Evaluate side-chains
  126 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain B residue   16 ASN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   85 SER
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   33 LEU
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  149 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 63 optimal weight:    7.9990
   chunk 97 optimal weight:    3.9990
   chunk 71 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   chunk 38 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
N  77 ASN
R 119 GLN
R 154 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.156630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.111297 restraints weight = 18164.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 3.34
r_work: 0.3138 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3099
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3099 r_free = 0.3099    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3099 r_free = 0.3099    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3099
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.3013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8259  Z= 0.170
  Angle     :  0.523   7.400  11232  Z= 0.262
  Chirality :  0.042   0.198   1265
  Planarity :  0.004   0.049   1428
  Dihedral  :  6.513  84.173   1332
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 17.50 %
    Favored  : 79.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.27 (0.27), residues: 1016
  helix:  2.56 (0.26), residues: 404
  sheet:  0.28 (0.35), residues: 228
  loop : -0.68 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 281 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.015   0.001   PHE N 108 
 TYR   0.018   0.001   TYR A 339 
 ARG   0.012   0.000   ARG B  19 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8514 (mtmt)
REVERT: B   14 LEU cc_start: 0.7921 (mt) cc_final: 0.7490 (mp)
REVERT: B   78 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8107 (mmtm)
REVERT: B   96 ARG cc_start: 0.7754 (ttt180) cc_final: 0.7485 (ttm170)
REVERT: B  212 ASP cc_start: 0.8113 (t70) cc_final: 0.7591 (t70)
REVERT: B  217 MET cc_start: 0.8196 (ptt) cc_final: 0.7822 (pmm)
REVERT: B  226 GLU cc_start: 0.8325 (pt0) cc_final: 0.7818 (pt0)
REVERT: B  228 ASP cc_start: 0.8385 (p0) cc_final: 0.8062 (p0)
REVERT: B  270 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7930 (pp)
REVERT: B  280 LYS cc_start: 0.8645 (tttm) cc_final: 0.8402 (ttpt)
REVERT: G   21 MET cc_start: 0.7405 (tpt) cc_final: 0.6867 (mmm)
REVERT: N    5 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7370 (mm-40)
REVERT: N   60 TYR cc_start: 0.9048 (m-80) cc_final: 0.8698 (m-80)
REVERT: R   27 LEU cc_start: 0.7179 (mp) cc_final: 0.6930 (tt)
REVERT: R   97 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7481 (mt)
REVERT: R  146 TRP cc_start: 0.6868 (OUTLIER) cc_final: 0.5555 (m-10)
  outliers start: 25
  outliers final: 15
  residues processed: 125
  average time/residue: 1.0899
  time to fit residues: 145.8857
Evaluate side-chains
  129 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain B residue   16 ASN
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   85 SER
Chi-restraints excluded: chain R residue   33 LEU
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  146 TRP
Chi-restraints excluded: chain R residue  149 TRP
Chi-restraints excluded: chain R residue  231 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 75 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 63 optimal weight:    7.9990
   chunk 78 optimal weight:    0.0270
   chunk 35 optimal weight:    5.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
N  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.157801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.114428 restraints weight = 13397.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 2.88
r_work: 0.3169 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3152
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3152
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.3067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8259  Z= 0.142
  Angle     :  0.505   7.653  11232  Z= 0.252
  Chirality :  0.041   0.195   1265
  Planarity :  0.004   0.052   1428
  Dihedral  :  6.406  83.366   1332
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 17.38 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.36 (0.27), residues: 1016
  helix:  2.67 (0.26), residues: 404
  sheet:  0.30 (0.36), residues: 223
  loop : -0.64 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 281 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.010   0.001   PHE N 108 
 TYR   0.017   0.001   TYR A 339 
 ARG   0.012   0.000   ARG B  19 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.834 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8471 (mtmt)
REVERT: A  392 GLU cc_start: 0.8256 (tp30) cc_final: 0.7819 (mm-30)
REVERT: B   14 LEU cc_start: 0.7874 (mt) cc_final: 0.7448 (mp)
REVERT: B   78 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8051 (mmtm)
REVERT: B   96 ARG cc_start: 0.7712 (ttt180) cc_final: 0.7437 (ttm170)
REVERT: B  212 ASP cc_start: 0.8074 (t70) cc_final: 0.7563 (t70)
REVERT: B  215 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7408 (mm-30)
REVERT: B  217 MET cc_start: 0.8131 (ptt) cc_final: 0.7736 (pmm)
REVERT: B  226 GLU cc_start: 0.8299 (pt0) cc_final: 0.7784 (pt0)
REVERT: B  228 ASP cc_start: 0.8342 (p0) cc_final: 0.8027 (p0)
REVERT: B  270 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7877 (pp)
REVERT: B  280 LYS cc_start: 0.8620 (tttm) cc_final: 0.8344 (ttpt)
REVERT: G   21 MET cc_start: 0.7385 (tpt) cc_final: 0.6829 (mmm)
REVERT: N   60 TYR cc_start: 0.9049 (m-80) cc_final: 0.8678 (m-80)
REVERT: R   27 LEU cc_start: 0.6997 (mp) cc_final: 0.6751 (tt)
REVERT: R   79 ARG cc_start: 0.8359 (tpp80) cc_final: 0.7412 (tpm170)
REVERT: R   97 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7392 (mt)
REVERT: R  146 TRP cc_start: 0.6817 (OUTLIER) cc_final: 0.5511 (m-10)
  outliers start: 25
  outliers final: 15
  residues processed: 125
  average time/residue: 1.0662
  time to fit residues: 142.7772
Evaluate side-chains
  129 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain B residue   16 ASN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   85 SER
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   33 LEU
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  146 TRP
Chi-restraints excluded: chain R residue  149 TRP
Chi-restraints excluded: chain R residue  231 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 97 optimal weight:    0.0050
   chunk 85 optimal weight:    0.4980
   chunk 72 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 32 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0670
   chunk 36 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.4532

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

Flipped N/Q/H residues before XYZ refinement:
N  77 ASN
R 119 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.159143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.122659 restraints weight = 16206.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 4.15
r_work: 0.3136 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3116
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3116 r_free = 0.3116    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3116 r_free = 0.3116    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3116
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.3240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8259  Z= 0.137
  Angle     :  0.519  11.342  11232  Z= 0.254
  Chirality :  0.041   0.190   1265
  Planarity :  0.004   0.053   1428
  Dihedral  :  6.281  82.547   1332
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.10 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.49 (0.27), residues: 1016
  helix:  2.77 (0.26), residues: 404
  sheet:  0.29 (0.37), residues: 217
  loop : -0.49 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 281 
 HIS   0.002   0.001   HIS A 220 
 PHE   0.009   0.001   PHE B 241 
 TYR   0.016   0.001   TYR A 339 
 ARG   0.013   0.000   ARG B  19 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.819 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8589 (mtmt)
REVERT: B   14 LEU cc_start: 0.7835 (mt) cc_final: 0.7419 (mp)
REVERT: B   29 THR cc_start: 0.8388 (m) cc_final: 0.8078 (p)
REVERT: B   78 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8063 (mmtm)
REVERT: B   96 ARG cc_start: 0.7800 (ttt180) cc_final: 0.7490 (ttm170)
REVERT: B  212 ASP cc_start: 0.8106 (t70) cc_final: 0.7612 (t70)
REVERT: B  214 ARG cc_start: 0.7593 (mtm110) cc_final: 0.7390 (mtm110)
REVERT: B  215 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7434 (mm-30)
REVERT: B  217 MET cc_start: 0.8196 (ptt) cc_final: 0.7750 (pmm)
REVERT: B  226 GLU cc_start: 0.8392 (pt0) cc_final: 0.7995 (pt0)
REVERT: B  228 ASP cc_start: 0.8332 (p0) cc_final: 0.8015 (p0)
REVERT: B  270 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7901 (pp)
REVERT: B  280 LYS cc_start: 0.8575 (tttm) cc_final: 0.8331 (ttpt)
REVERT: G   21 MET cc_start: 0.7325 (tpt) cc_final: 0.6805 (mmm)
REVERT: N   59 SER cc_start: 0.7845 (OUTLIER) cc_final: 0.7522 (t)
REVERT: N   60 TYR cc_start: 0.9077 (m-80) cc_final: 0.8719 (m-80)
REVERT: R   27 LEU cc_start: 0.7015 (mp) cc_final: 0.6745 (tt)
REVERT: R   97 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7466 (mt)
  outliers start: 19
  outliers final: 11
  residues processed: 128
  average time/residue: 1.0819
  time to fit residues: 148.1174
Evaluate side-chains
  128 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain B residue   16 ASN
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   33 LEU
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  149 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 90 optimal weight:    0.9990
   chunk 88 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 50 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
B  35 ASN
B 259 GLN
N  77 ASN
R 119 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.157524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.113649 restraints weight = 22779.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 4.22
r_work: 0.3092 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3084
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3084
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.3229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8259  Z= 0.177
  Angle     :  0.533  10.109  11232  Z= 0.264
  Chirality :  0.042   0.196   1265
  Planarity :  0.004   0.056   1428
  Dihedral  :  6.312  83.155   1332
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 18.57 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.42 (0.27), residues: 1016
  helix:  2.74 (0.26), residues: 404
  sheet:  0.18 (0.36), residues: 217
  loop : -0.52 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 281 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.013   0.001   PHE N 108 
 TYR   0.018   0.001   TYR A 339 
 ARG   0.013   0.000   ARG B  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5853.64 seconds
wall clock time: 103 minutes 43.24 seconds (6223.24 seconds total)