Starting phenix.real_space_refine
on Wed Mar 12 18:23:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7cfm_30344/03_2025/7cfm_30344.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7cfm_30344/03_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_30344/03_2025/7cfm_30344.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7cfm_30344/03_2025/7cfm_30344.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7cfm_30344/03_2025/7cfm_30344.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7cfm_30344/03_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-5624/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: 10.54, per 1000 atoms: 1.30
  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: 3.10
  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: 1.78
  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: 3.00

  Time building geometry restraints manager: 3.52 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:             84.140
  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:          0.330
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     31.640
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:56.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:  173.170
-------------------------------------------------------------------------------
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  : 0.899 
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: 1.2076
  time to fit residues: 240.1851
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  : 0.867 
-------------------------------------------------------------------------------
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 = 0.118464 restraints weight = 18269.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 3.64
r_work: 0.3190 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3168
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3168
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
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  : 0.988 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.7064 (ptp90)
REVERT: A  378 ASP cc_start: 0.7634 (m-30) cc_final: 0.7413 (m-30)
REVERT: B   14 LEU cc_start: 0.7876 (mt) cc_final: 0.7431 (mp)
REVERT: B  212 ASP cc_start: 0.8159 (t70) cc_final: 0.7762 (t70)
REVERT: B  217 MET cc_start: 0.8110 (ptt) cc_final: 0.7428 (pmt)
REVERT: B  270 ILE cc_start: 0.8244 (pp) cc_final: 0.7843 (pp)
REVERT: B  280 LYS cc_start: 0.8694 (tttm) cc_final: 0.8411 (ttpt)
REVERT: G   21 MET cc_start: 0.7587 (tpt) cc_final: 0.6948 (mmm)
REVERT: R   27 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6963 (tt)
  outliers start: 26
  outliers final: 8
  residues processed: 148
  average time/residue: 1.1170
  time to fit residues: 176.6662
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  : 0.959 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 44 optimal weight:    0.3980
   chunk 16 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.0586

-------------------------------------------------------------------------------
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 = 0.3831 r_free = 0.3831 target = 0.159888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.116055 restraints weight = 21624.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 4.14
r_work: 0.3128 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3086
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3086 r_free = 0.3086    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3086 r_free = 0.3086    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3086
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.2213

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= 0.206
  Angle     :  0.578   8.668  11232  Z= 0.287
  Chirality :  0.043   0.193   1265
  Planarity :  0.004   0.059   1428
  Dihedral  :  7.156  86.904   1332
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 14.29 %
    Favored  : 82.38 %
  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:  0.21 (0.26), residues: 1016
  helix:  1.76 (0.26), residues: 392
  sheet: -0.37 (0.35), residues: 221
  loop : -1.18 (0.29), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 281 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.020   0.001   PHE N 108 
 TYR   0.022   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
  142 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 114
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8537 (mttp)
REVERT: A  317 ARG cc_start: 0.7358 (ptp-110) cc_final: 0.7123 (ptp90)
REVERT: A  392 GLU cc_start: 0.8397 (tp30) cc_final: 0.8039 (mm-30)
REVERT: B  212 ASP cc_start: 0.8119 (t70) cc_final: 0.7543 (t70)
REVERT: B  215 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7334 (mm-30)
REVERT: B  217 MET cc_start: 0.8266 (ptt) cc_final: 0.7483 (pmt)
REVERT: B  226 GLU cc_start: 0.8366 (pt0) cc_final: 0.7714 (pt0)
REVERT: B  262 MET cc_start: 0.8562 (ttp) cc_final: 0.8311 (ptm)
REVERT: B  270 ILE cc_start: 0.8269 (pp) cc_final: 0.7872 (pp)
REVERT: B  280 LYS cc_start: 0.8669 (tttm) cc_final: 0.8374 (ttpt)
REVERT: G   21 MET cc_start: 0.7647 (tpt) cc_final: 0.7107 (mmm)
REVERT: N    5 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7285 (mm110)
REVERT: R   27 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6970 (mp)
REVERT: R  252 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8503 (mm-30)
  outliers start: 28
  outliers final: 10
  residues processed: 132
  average time/residue: 1.0132
  time to fit residues: 143.5471
Evaluate side-chains
  122 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  270 LEU
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  286 LEU
Chi-restraints excluded: chain N residue    5 GLN
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 62 optimal weight:    9.9990
   chunk 2 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 78 optimal weight:    0.8980
   chunk 85 optimal weight:    7.9990
   chunk 81 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 44 optimal weight:    3.9990
   overall best weight:    1.3184

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.155617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.110710 restraints weight = 17800.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 3.28
r_work: 0.3070 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3072
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3072 r_free = 0.3072    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 = 0.3072 r_free = 0.3072    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3072
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2485

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= 0.227
  Angle     :  0.574   8.422  11232  Z= 0.286
  Chirality :  0.044   0.201   1265
  Planarity :  0.004   0.040   1428
  Dihedral  :  6.934  87.915   1332
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 14.29 %
    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:  0.53 (0.26), residues: 1016
  helix:  2.10 (0.26), residues: 386
  sheet: -0.20 (0.35), residues: 221
  loop : -1.04 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 281 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.021   0.002   PHE N 108 
 TYR   0.023   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: 37
    poor density    : 112
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8557 (mttp)
REVERT: A  392 GLU cc_start: 0.8371 (tp30) cc_final: 0.7939 (mm-30)
REVERT: B  212 ASP cc_start: 0.8199 (t70) cc_final: 0.7620 (t70)
REVERT: B  215 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7314 (mm-30)
REVERT: B  217 MET cc_start: 0.8266 (ptt) cc_final: 0.7529 (ppp)
REVERT: B  226 GLU cc_start: 0.8357 (pt0) cc_final: 0.7820 (pt0)
REVERT: B  270 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7890 (pp)
REVERT: B  280 LYS cc_start: 0.8715 (tttm) cc_final: 0.8420 (ttpt)
REVERT: G   21 MET cc_start: 0.7599 (tpt) cc_final: 0.7044 (mmm)
REVERT: R   97 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7434 (mt)
REVERT: R  154 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.7978 (m110)
REVERT: R  252 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8433 (mm-30)
  outliers start: 37
  outliers final: 14
  residues processed: 135
  average time/residue: 1.1131
  time to fit residues: 160.7671
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  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   16 ASN
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  200 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 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
Chi-restraints excluded: chain R residue  231 LEU
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:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 62 optimal weight:    0.4980
   chunk 93 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 37 optimal weight:    0.7980
   chunk 95 optimal weight:    0.7980
   chunk 90 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0970
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.3813 r_free = 0.3813 target = 0.158591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.120741 restraints weight = 15775.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 3.66
r_work: 0.3159 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3138
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3138 r_free = 0.3138    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3138 r_free = 0.3138    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3138
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.2700

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= 0.146
  Angle     :  0.532  10.048  11232  Z= 0.259
  Chirality :  0.042   0.194   1265
  Planarity :  0.004   0.041   1428
  Dihedral  :  6.736  89.841   1332
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 16.07 %
    Favored  : 80.71 %
  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:  0.93 (0.27), residues: 1016
  helix:  2.38 (0.26), residues: 394
  sheet:  0.05 (0.36), residues: 222
  loop : -0.86 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 281 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.010   0.001   PHE B 241 
 TYR   0.017   0.001   TYR A 339 
 ARG   0.011   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
  141 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 114
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8595 (mttp)
REVERT: A  392 GLU cc_start: 0.8286 (tp30) cc_final: 0.7899 (mm-30)
REVERT: B   14 LEU cc_start: 0.7897 (mt) cc_final: 0.7456 (mp)
REVERT: B   78 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8127 (mmtm)
REVERT: B   96 ARG cc_start: 0.7829 (ttt-90) cc_final: 0.7585 (ttm110)
REVERT: B  212 ASP cc_start: 0.8158 (t70) cc_final: 0.7549 (t70)
REVERT: B  215 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7259 (mm-30)
REVERT: B  217 MET cc_start: 0.8077 (ptt) cc_final: 0.7381 (pmt)
REVERT: B  226 GLU cc_start: 0.8326 (pt0) cc_final: 0.7823 (pt0)
REVERT: B  228 ASP cc_start: 0.8335 (p0) cc_final: 0.7944 (p0)
REVERT: B  270 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7898 (pp)
REVERT: B  280 LYS cc_start: 0.8669 (tttm) cc_final: 0.8437 (ttpt)
REVERT: G   21 MET cc_start: 0.7427 (tpt) cc_final: 0.6919 (mmm)
REVERT: R  154 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7915 (m-40)
  outliers start: 27
  outliers final: 14
  residues processed: 129
  average time/residue: 1.0618
  time to fit residues: 147.4091
Evaluate side-chains
  125 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  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   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   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  149 TRP
Chi-restraints excluded: chain R residue  154 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 95 optimal weight:    0.6980
   chunk 66 optimal weight:    0.0040
   chunk 10 optimal weight:    0.9980
   chunk 24 optimal weight:    7.9990
   chunk 67 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 55 optimal weight:    0.0570
   chunk 83 optimal weight:    0.0010
   chunk 16 optimal weight:    8.9990
   chunk 48 optimal weight:    0.0470
   chunk 70 optimal weight:    6.9990
   overall best weight:    0.1614

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.160222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.115517 restraints weight = 25228.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 4.33
r_work: 0.3145 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3110
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    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 = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3110
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.2865

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= 0.122
  Angle     :  0.508  10.008  11232  Z= 0.248
  Chirality :  0.041   0.191   1265
  Planarity :  0.004   0.044   1428
  Dihedral  :  6.584  87.247   1332
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 16.90 %
    Favored  : 80.36 %
  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:  1.31 (0.27), residues: 1016
  helix:  2.76 (0.26), residues: 385
  sheet:  0.23 (0.36), residues: 221
  loop : -0.62 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 281 
 HIS   0.002   0.000   HIS A 220 
 PHE   0.009   0.001   PHE B 241 
 TYR   0.016   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
  139 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8531 (mtmt)
REVERT: A  392 GLU cc_start: 0.8298 (tp30) cc_final: 0.7896 (mm-30)
REVERT: B   14 LEU cc_start: 0.7812 (mt) cc_final: 0.7379 (mp)
REVERT: B   96 ARG cc_start: 0.7834 (ttt-90) cc_final: 0.7573 (ttm110)
REVERT: B  212 ASP cc_start: 0.8067 (t70) cc_final: 0.7432 (t70)
REVERT: B  215 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7174 (mm-30)
REVERT: B  217 MET cc_start: 0.8090 (ptt) cc_final: 0.7292 (pmt)
REVERT: B  226 GLU cc_start: 0.8375 (pt0) cc_final: 0.7875 (pt0)
REVERT: B  228 ASP cc_start: 0.8337 (p0) cc_final: 0.7956 (p0)
REVERT: B  270 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7899 (pp)
REVERT: B  280 LYS cc_start: 0.8594 (tttm) cc_final: 0.8292 (ttpt)
REVERT: G   21 MET cc_start: 0.7394 (tpt) cc_final: 0.6879 (mmm)
REVERT: R   97 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7412 (mt)
  outliers start: 23
  outliers final: 12
  residues processed: 130
  average time/residue: 1.1569
  time to fit residues: 160.7290
Evaluate side-chains
  124 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
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  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   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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 8 optimal weight:    0.1980
   chunk 39 optimal weight:    3.9990
   chunk 80 optimal weight:    0.5980
   chunk 16 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 52 optimal weight:    8.9990
   chunk 50 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 88 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    0.7584

-------------------------------------------------------------------------------
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  32 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 = 0.3816 r_free = 0.3816 target = 0.158931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.113672 restraints weight = 18316.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 3.35
r_work: 0.3158 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3120
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3120
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.2913

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= 0.159
  Angle     :  0.511   7.290  11232  Z= 0.253
  Chirality :  0.042   0.198   1265
  Planarity :  0.004   0.045   1428
  Dihedral  :  6.547  85.093   1332
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 17.26 %
    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:  1.34 (0.27), residues: 1016
  helix:  2.77 (0.26), residues: 391
  sheet:  0.26 (0.36), residues: 222
  loop : -0.64 (0.30), residues: 403

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   0.014   0.001   PHE N 108 
 TYR   0.018   0.001   TYR A 339 
 ARG   0.011   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
  139 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8522 (mtmt)
REVERT: A  392 GLU cc_start: 0.8316 (tp30) cc_final: 0.7894 (mm-30)
REVERT: B   14 LEU cc_start: 0.7912 (mt) cc_final: 0.7479 (mp)
REVERT: B   96 ARG cc_start: 0.7881 (ttt-90) cc_final: 0.7644 (ttm170)
REVERT: B  212 ASP cc_start: 0.8137 (t70) cc_final: 0.7638 (t70)
REVERT: B  217 MET cc_start: 0.8107 (ptt) cc_final: 0.7760 (pmm)
REVERT: B  226 GLU cc_start: 0.8342 (pt0) cc_final: 0.7870 (pt0)
REVERT: B  228 ASP cc_start: 0.8417 (p0) cc_final: 0.8105 (p0)
REVERT: B  270 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7932 (pp)
REVERT: B  280 LYS cc_start: 0.8696 (tttm) cc_final: 0.8346 (ttpt)
REVERT: G   21 MET cc_start: 0.7412 (tpt) cc_final: 0.6866 (mmm)
REVERT: N    5 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7352 (mm-40)
REVERT: N   60 TYR cc_start: 0.9026 (m-80) cc_final: 0.8736 (m-80)
REVERT: R   27 LEU cc_start: 0.7099 (mp) cc_final: 0.6879 (tt)
REVERT: R   97 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7494 (mt)
  outliers start: 27
  outliers final: 16
  residues processed: 129
  average time/residue: 0.9926
  time to fit residues: 137.5800
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  : 0.830 
-------------------------------------------------------------------------------
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  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 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  118 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:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 63 optimal weight:    7.9990
   chunk 97 optimal weight:    6.9990
   chunk 71 optimal weight:    0.2980
   chunk 91 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   chunk 39 optimal weight:    6.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.158104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.112983 restraints weight = 18073.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 3.29
r_work: 0.3110 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3087
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3087 r_free = 0.3087    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 = 0.3087 r_free = 0.3087    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3087
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.3019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8259  Z= 0.191
  Angle     :  0.540   7.368  11232  Z= 0.270
  Chirality :  0.042   0.203   1265
  Planarity :  0.004   0.046   1428
  Dihedral  :  6.587  84.559   1332
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 17.62 %
    Favored  : 79.05 %
  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:  1.25 (0.27), residues: 1016
  helix:  2.55 (0.26), residues: 407
  sheet:  0.17 (0.36), residues: 223
  loop : -0.65 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 281 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.017   0.001   PHE N 108 
 TYR   0.019   0.001   TYR A 339 
 ARG   0.013   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
  141 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 113
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8520 (mtmt)
REVERT: A  392 GLU cc_start: 0.8351 (tp30) cc_final: 0.8028 (mm-30)
REVERT: B   14 LEU cc_start: 0.7905 (mt) cc_final: 0.7479 (mp)
REVERT: B   96 ARG cc_start: 0.7921 (ttt-90) cc_final: 0.7583 (ttm170)
REVERT: B  212 ASP cc_start: 0.8090 (t70) cc_final: 0.7572 (t70)
REVERT: B  215 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7433 (mm-30)
REVERT: B  217 MET cc_start: 0.8181 (ptt) cc_final: 0.7772 (pmm)
REVERT: B  226 GLU cc_start: 0.8339 (pt0) cc_final: 0.7809 (pt0)
REVERT: B  228 ASP cc_start: 0.8414 (p0) cc_final: 0.8089 (p0)
REVERT: B  270 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7910 (pp)
REVERT: B  280 LYS cc_start: 0.8638 (tttm) cc_final: 0.8430 (ttpt)
REVERT: G   21 MET cc_start: 0.7383 (tpt) cc_final: 0.6894 (mmm)
REVERT: N    5 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7327 (mm-40)
REVERT: N   60 TYR cc_start: 0.9042 (m-80) cc_final: 0.8787 (m-80)
REVERT: R   97 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7511 (mt)
REVERT: R  146 TRP cc_start: 0.7038 (OUTLIER) cc_final: 0.5794 (m-10)
  outliers start: 28
  outliers final: 16
  residues processed: 130
  average time/residue: 1.0687
  time to fit residues: 149.2383
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  : 0.875 
-------------------------------------------------------------------------------
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  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    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 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  118 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:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   chunk 75 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 18 optimal weight:    0.2980
   chunk 29 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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 = 0.3810 r_free = 0.3810 target = 0.158545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.115226 restraints weight = 13250.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 2.88
r_work: 0.3185 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3153
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3153
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.3103

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= 0.152
  Angle     :  0.519   8.995  11232  Z= 0.257
  Chirality :  0.041   0.197   1265
  Planarity :  0.004   0.050   1428
  Dihedral  :  6.479  84.015   1332
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.69 %
    Favored  : 79.05 %
  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:  1.48 (0.27), residues: 1016
  helix:  2.81 (0.26), residues: 397
  sheet:  0.33 (0.35), residues: 229
  loop : -0.56 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 281 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.011   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
  132 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8504 (mtmt)
REVERT: A  392 GLU cc_start: 0.8267 (tp30) cc_final: 0.7845 (mm-30)
REVERT: B   14 LEU cc_start: 0.7930 (mt) cc_final: 0.7505 (mp)
REVERT: B   29 THR cc_start: 0.8459 (m) cc_final: 0.8147 (p)
REVERT: B   96 ARG cc_start: 0.7899 (ttt-90) cc_final: 0.7598 (ttm170)
REVERT: B  212 ASP cc_start: 0.8132 (t70) cc_final: 0.7654 (t70)
REVERT: B  217 MET cc_start: 0.8145 (ptt) cc_final: 0.7777 (pmm)
REVERT: B  226 GLU cc_start: 0.8296 (pt0) cc_final: 0.7932 (pt0)
REVERT: B  228 ASP cc_start: 0.8356 (p0) cc_final: 0.8070 (p0)
REVERT: B  270 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7890 (pp)
REVERT: B  280 LYS cc_start: 0.8678 (tttm) cc_final: 0.8412 (ttpt)
REVERT: B  323 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8329 (p0)
REVERT: G   21 MET cc_start: 0.7350 (tpt) cc_final: 0.6789 (mmm)
REVERT: N   60 TYR cc_start: 0.9060 (m-80) cc_final: 0.8742 (m-80)
REVERT: R   97 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7512 (mt)
REVERT: R  146 TRP cc_start: 0.6901 (OUTLIER) cc_final: 0.5564 (m-10)
  outliers start: 19
  outliers final: 13
  residues processed: 125
  average time/residue: 1.0673
  time to fit residues: 143.1468
Evaluate side-chains
  131 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
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  100 VAL
Chi-restraints excluded: chain B residue  198 LEU
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 B residue  323 ASP
Chi-restraints excluded: chain N residue   59 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 97 optimal weight:    0.0570
   chunk 85 optimal weight:    0.0370
   chunk 72 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.4576

-------------------------------------------------------------------------------
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 = 0.3810 r_free = 0.3810 target = 0.158486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.114416 restraints weight = 16190.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 3.13
r_work: 0.3168 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3158
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3158 r_free = 0.3158    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3158 r_free = 0.3158    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3158
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.3224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8259  Z= 0.137
  Angle     :  0.514   9.326  11232  Z= 0.254
  Chirality :  0.041   0.193   1265
  Planarity :  0.004   0.052   1428
  Dihedral  :  6.336  83.115   1332
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 18.69 %
    Favored  : 78.81 %
  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:  1.65 (0.27), residues: 1016
  helix:  2.94 (0.26), residues: 397
  sheet:  0.43 (0.36), residues: 228
  loop : -0.44 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 281 
 HIS   0.002   0.001   HIS A 220 
 PHE   0.010   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
  139 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8578 (mtmt)
REVERT: B   14 LEU cc_start: 0.7885 (mt) cc_final: 0.7472 (mp)
REVERT: B   29 THR cc_start: 0.8490 (m) cc_final: 0.8176 (p)
REVERT: B   96 ARG cc_start: 0.7904 (ttt-90) cc_final: 0.7588 (ttm170)
REVERT: B  212 ASP cc_start: 0.8080 (t70) cc_final: 0.7612 (t70)
REVERT: B  217 MET cc_start: 0.8161 (ptt) cc_final: 0.7756 (pmm)
REVERT: B  226 GLU cc_start: 0.8309 (pt0) cc_final: 0.7856 (pt0)
REVERT: B  228 ASP cc_start: 0.8317 (p0) cc_final: 0.8047 (p0)
REVERT: B  270 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7848 (pp)
REVERT: G   21 MET cc_start: 0.7320 (tpt) cc_final: 0.6803 (mmm)
REVERT: N   59 SER cc_start: 0.7792 (OUTLIER) cc_final: 0.7474 (t)
REVERT: N   60 TYR cc_start: 0.9062 (m-80) cc_final: 0.8739 (m-80)
REVERT: R   97 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7449 (mt)
  outliers start: 21
  outliers final: 13
  residues processed: 131
  average time/residue: 1.0385
  time to fit residues: 146.0668
Evaluate side-chains
  127 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
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   97 SER
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  149 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 90 optimal weight:    0.6980
   chunk 88 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 14 optimal weight:    8.9990
   chunk 42 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.4582

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

Flipped N/Q/H residues before XYZ refinement:
B  35 ASN
N  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.154877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.110429 restraints weight = 22798.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 4.22
r_work: 0.3074 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.3232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8259  Z= 0.237
  Angle     :  0.578  11.102  11232  Z= 0.285
  Chirality :  0.043   0.204   1265
  Planarity :  0.004   0.053   1428
  Dihedral  :  6.512  84.475   1332
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 18.69 %
    Favored  : 78.69 %
  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:  1.30 (0.27), residues: 1016
  helix:  2.55 (0.26), residues: 407
  sheet:  0.17 (0.35), residues: 223
  loop : -0.54 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 281 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.019   0.002   PHE N 108 
 TYR   0.020   0.001   TYR A 339 
 ARG   0.014   0.001   ARG B  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6629.16 seconds
wall clock time: 116 minutes 28.34 seconds (6988.34 seconds total)