Starting phenix.real_space_refine
on Tue Feb 11 07:39:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y5h_33620/02_2025/7y5h_33620.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y5h_33620/02_2025/7y5h_33620.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y5h_33620/02_2025/7y5h_33620.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y5h_33620/02_2025/7y5h_33620.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y5h_33620/02_2025/7y5h_33620.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y5h_33620/02_2025/7y5h_33620.cif"
  }
  resolution = 3.72
  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=   0.019 sd=   0.082
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      4      6.06       5
     S      30      5.16       5
     C    3066      2.51       5
     N     778      2.21       5
     O     826      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4704
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2350
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 300, 2350
          Classifications: {'peptide': 300}
          Link IDs: {'PTRANS': 8, 'TRANS': 291}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 2350
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 300, 2350
          Classifications: {'peptide': 300}
          Link IDs: {'PTRANS': 8, 'TRANS': 291}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2387  SG  CYS A  46      27.718  33.935  76.919  1.00 43.42           S
  ATOM   4663  SG  CYS A 366      55.725  40.607  76.131  1.00 59.27           S
  ATOM   4688  SG  CYS A 369      52.369  42.490  75.334  1.00 55.45           S
  ATOM   2313  SG  CYS B 366      20.829  30.217  75.781  1.00 59.27           S
  ATOM   2338  SG  CYS B 369      24.407  28.745  75.218  1.00 55.45           S
  ATOM     37  SG  CYS B  46      48.769  37.462  77.024  1.00 43.42           S

  Time building chain proxies: 3.38, per 1000 atoms: 0.72
  Number of scatterers: 4704
  At special positions: 0
  Unit cell: (77.35, 73.1, 102, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      4     29.99
     S      30     16.00
     O     826      8.00
     N     778      7.00
     C    3066      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Conformation dependent library (CDL) restraints added in 531.2 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 401 "
        pdb="ZN    ZN A 401 " - pdb=" NE2 HIS A  45 "
        pdb="ZN    ZN A 401 " - pdb=" ND1 HIS A  47 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS B 369 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS B 366 "
      pdb="  ZN A 402 "
        pdb="ZN    ZN A 402 " - pdb=" ND1 HIS A 323 "
        pdb="ZN    ZN A 402 " - pdb=" NE2 HIS A 306 "
        pdb="ZN    ZN A 402 " - pdb=" SG  CYS B  46 "
      pdb="  ZN B 401 "
        pdb="ZN    ZN B 401 " - pdb=" ND1 HIS B 323 "
        pdb="ZN    ZN B 401 " - pdb=" NE2 HIS B 306 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS A  46 "
      pdb="  ZN B 402 "
        pdb="ZN    ZN B 402 " - pdb=" NE2 HIS B  45 "
        pdb="ZN    ZN B 402 " - pdb=" ND1 HIS B  47 "
        pdb="ZN    ZN B 402 " - pdb=" SG  CYS A 369 "
        pdb="ZN    ZN B 402 " - pdb=" SG  CYS A 366 "
      Number of angles added : 2


  1168 Ramachandran restraints generated.
    584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1156

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 2 sheets defined
      68.8% alpha, 9.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'B' and resid 47 through 50
    Processing helix  chain 'B' and resid 51 through 88
      removed outlier: 3.830A  pdb=" N   ALA B  56 " --> pdb=" O   LYS B  52 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ARG B  57 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LYS B  67 " --> pdb=" O   PHE B  63 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   CYS B  69 " --> pdb=" O   LYS B  65 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ALA B  81 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   GLU B  82 " --> pdb=" O   PHE B  78 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ILE B  83 " --> pdb=" O   ILE B  79 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   TYR B  87 " --> pdb=" O   ILE B  83 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ILE B  88 " --> pdb=" O   VAL B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 118
      removed outlier: 4.303A  pdb=" N   HIS B 100 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   LEU B 101 " --> pdb=" O   ASP B  97 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LEU B 102 " --> pdb=" O   ALA B  98 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL B 103 " --> pdb=" O   ALA B  99 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE B 110 " --> pdb=" O   SER B 106 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   SER B 111 " --> pdb=" O   SER B 107 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LEU B 112 " --> pdb=" O   PHE B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 131
      No H-bonds generated for 'chain 'B' and resid 129 through 131'
    Processing helix  chain 'B' and resid 132 through 158
      removed outlier: 3.628A  pdb=" N   LEU B 136 " --> pdb=" O   ARG B 132 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ALA B 138 " --> pdb=" O   GLU B 134 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   SER B 141 " --> pdb=" O   GLY B 137 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE B 145 " --> pdb=" O   SER B 141 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   TRP B 146 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 191
      removed outlier: 3.567A  pdb=" N   LEU B 184 " --> pdb=" O   LEU B 180 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU B 188 " --> pdb=" O   LEU B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 218 through 229
      removed outlier: 4.092A  pdb=" N   ILE B 224 " --> pdb=" O   ARG B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 246
      removed outlier: 3.509A  pdb=" N   SER B 233 " --> pdb=" O   ASP B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 268
      removed outlier: 3.612A  pdb=" N   ILE B 255 " --> pdb=" O   MET B 251 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   THR B 257 " --> pdb=" O   ASP B 253 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   PHE B 258 " --> pdb=" O   PRO B 254 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ILE B 262 " --> pdb=" O   PHE B 258 " (cutoff:3.500A)
      removed outlier: 5.010A  pdb=" N   PHE B 263 " --> pdb=" O   ILE B 259 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   VAL B 264 " --> pdb=" O   PHE B 260 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LEU B 265 " --> pdb=" O   SER B 261 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   THR B 268 " --> pdb=" O   VAL B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 280
      removed outlier: 3.558A  pdb=" N   LEU B 272 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ASP B 274 " --> pdb=" O   THR B 270 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   VAL B 278 " --> pdb=" O   ASP B 274 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   LEU B 279 " --> pdb=" O   LEU B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 298
    Processing helix  chain 'B' and resid 331 through 345
      removed outlier: 4.016A  pdb=" N   ILE B 335 " --> pdb=" O   GLU B 331 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU B 336 " --> pdb=" O   SER B 332 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LYS B 337 " --> pdb=" O   LYS B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 362
      No H-bonds generated for 'chain 'B' and resid 360 through 362'
    Processing helix  chain 'A' and resid 47 through 50
    Processing helix  chain 'A' and resid 51 through 88
      removed outlier: 3.805A  pdb=" N   ALA A  56 " --> pdb=" O   LYS A  52 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ARG A  57 " --> pdb=" O   ALA A  53 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS A  67 " --> pdb=" O   PHE A  63 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   CYS A  69 " --> pdb=" O   LYS A  65 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ALA A  81 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLU A  82 " --> pdb=" O   PHE A  78 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ILE A  83 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   TYR A  87 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ILE A  88 " --> pdb=" O   VAL A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 118
      removed outlier: 3.946A  pdb=" N   HIS A 100 " --> pdb=" O   THR A  96 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ILE A 110 " --> pdb=" O   SER A 106 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   SER A 111 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LEU A 112 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 131
      No H-bonds generated for 'chain 'A' and resid 129 through 131'
    Processing helix  chain 'A' and resid 132 through 158
      removed outlier: 3.630A  pdb=" N   LEU A 136 " --> pdb=" O   ARG A 132 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ALA A 138 " --> pdb=" O   GLU A 134 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   SER A 141 " --> pdb=" O   GLY A 137 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ILE A 145 " --> pdb=" O   SER A 141 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   TRP A 146 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 191
      removed outlier: 3.557A  pdb=" N   LEU A 184 " --> pdb=" O   LEU A 180 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   LEU A 188 " --> pdb=" O   LEU A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 229
      removed outlier: 4.093A  pdb=" N   ILE A 224 " --> pdb=" O   ARG A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 246
      removed outlier: 3.528A  pdb=" N   SER A 233 " --> pdb=" O   ASP A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 267
      removed outlier: 3.601A  pdb=" N   ILE A 255 " --> pdb=" O   MET A 251 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   THR A 257 " --> pdb=" O   ASP A 253 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   PHE A 258 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ILE A 262 " --> pdb=" O   PHE A 258 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   PHE A 263 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   VAL A 264 " --> pdb=" O   PHE A 260 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LEU A 265 " --> pdb=" O   SER A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 280
      removed outlier: 3.560A  pdb=" N   LEU A 272 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ASP A 274 " --> pdb=" O   THR A 270 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   VAL A 278 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU A 279 " --> pdb=" O   LEU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 298
    Processing helix  chain 'A' and resid 331 through 345
      removed outlier: 4.020A  pdb=" N   ILE A 335 " --> pdb=" O   GLU A 331 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU A 336 " --> pdb=" O   SER A 332 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LYS A 337 " --> pdb=" O   LYS A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 362
      No H-bonds generated for 'chain 'A' and resid 360 through 362'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 302 through 314
      removed outlier: 6.801A  pdb=" N   ALA B 325 " --> pdb=" O   LYS B 303 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   VAL B 305 " --> pdb=" O   HIS B 323 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   HIS B 323 " --> pdb=" O   VAL B 305 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   SER B 307 " --> pdb=" O   SER B 321 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   SER B 321 " --> pdb=" O   SER B 307 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   HIS B 309 " --> pdb=" O   ILE B 319 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   ILE B 319 " --> pdb=" O   HIS B 309 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   TRP B 311 " --> pdb=" O   GLN B 317 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   GLN B 317 " --> pdb=" O   TRP B 311 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   VAL B 318 " --> pdb=" O   SER B 351 " (cutoff:3.500A)
      removed outlier: 8.937A  pdb=" N   THR B 353 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   LEU B 320 " --> pdb=" O   THR B 353 " (cutoff:3.500A)
      removed outlier: 8.315A  pdb=" N   GLN B 355 " --> pdb=" O   LEU B 320 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ALA B 322 " --> pdb=" O   GLN B 355 " (cutoff:3.500A)
      removed outlier: 8.037A  pdb=" N   GLU B 357 " --> pdb=" O   ALA B 322 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   ILE B 324 " --> pdb=" O   GLU B 357 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 302 through 314
      removed outlier: 6.803A  pdb=" N   ALA A 325 " --> pdb=" O   LYS A 303 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   VAL A 305 " --> pdb=" O   HIS A 323 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   HIS A 323 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   SER A 307 " --> pdb=" O   SER A 321 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   SER A 321 " --> pdb=" O   SER A 307 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   HIS A 309 " --> pdb=" O   ILE A 319 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ILE A 319 " --> pdb=" O   HIS A 309 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   TRP A 311 " --> pdb=" O   GLN A 317 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   GLN A 317 " --> pdb=" O   TRP A 311 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   VAL A 318 " --> pdb=" O   SER A 351 " (cutoff:3.500A)
      removed outlier: 8.949A  pdb=" N   THR A 353 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   LEU A 320 " --> pdb=" O   THR A 353 " (cutoff:3.500A)
      removed outlier: 8.334A  pdb=" N   GLN A 355 " --> pdb=" O   LEU A 320 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   ALA A 322 " --> pdb=" O   GLN A 355 " (cutoff:3.500A)
      removed outlier: 8.058A  pdb=" N   GLU A 357 " --> pdb=" O   ALA A 322 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   ILE A 324 " --> pdb=" O   GLU A 357 " (cutoff:3.500A)

    241 hydrogen bonds defined for protein.
    717 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.09

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1454
        1.34 -     1.46: 1054
        1.46 -     1.58: 2244
        1.58 -     1.69: 0
        1.69 -     1.81: 42
  Bond restraints: 4794
  Sorted by residual:
  bond pdb=" CB  GLU A 365 "
       pdb=" CG  GLU A 365 "
    ideal  model  delta    sigma   weight residual
    1.520  1.538 -0.018 3.00e-02 1.11e+03 3.59e-01
  bond pdb=" CG  LEU A 308 "
       pdb=" CD1 LEU A 308 "
    ideal  model  delta    sigma   weight residual
    1.521  1.505  0.016 3.30e-02 9.18e+02 2.21e-01
  bond pdb=" C   ASP A 253 "
       pdb=" N   PRO A 254 "
    ideal  model  delta    sigma   weight residual
    1.335  1.342 -0.006 1.36e-02 5.41e+03 2.17e-01
  bond pdb=" C   ASP B 253 "
       pdb=" N   PRO B 254 "
    ideal  model  delta    sigma   weight residual
    1.335  1.342 -0.006 1.36e-02 5.41e+03 2.16e-01
  bond pdb=" N   GLU B 281 "
       pdb=" CA  GLU B 281 "
    ideal  model  delta    sigma   weight residual
    1.460  1.466 -0.006 1.42e-02 4.96e+03 2.09e-01
  ... (remaining 4789 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.30: 6429
        1.30 -     2.61: 57
        2.61 -     3.91: 19
        3.91 -     5.22: 3
        5.22 -     6.52: 2
  Bond angle restraints: 6510
  Sorted by residual:
  angle pdb=" C   MET A 280 "
        pdb=" N   GLU A 281 "
        pdb=" CA  GLU A 281 "
      ideal   model   delta    sigma   weight residual
     122.82  125.84   -3.02 1.42e+00 4.96e-01 4.53e+00
  angle pdb=" C   MET B 280 "
        pdb=" N   GLU B 281 "
        pdb=" CA  GLU B 281 "
      ideal   model   delta    sigma   weight residual
     122.82  125.80   -2.98 1.42e+00 4.96e-01 4.40e+00
  angle pdb=" CA  LEU B 275 "
        pdb=" CB  LEU B 275 "
        pdb=" CG  LEU B 275 "
      ideal   model   delta    sigma   weight residual
     116.30  122.82   -6.52 3.50e+00 8.16e-02 3.47e+00
  angle pdb=" CA  LEU A 275 "
        pdb=" CB  LEU A 275 "
        pdb=" CG  LEU A 275 "
      ideal   model   delta    sigma   weight residual
     116.30  122.61   -6.31 3.50e+00 8.16e-02 3.25e+00
  angle pdb=" CA  GLU B 281 "
        pdb=" CB  GLU B 281 "
        pdb=" CG  GLU B 281 "
      ideal   model   delta    sigma   weight residual
     114.10  117.51   -3.41 2.00e+00 2.50e-01 2.90e+00
  ... (remaining 6505 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.72: 2531
       14.72 -    29.43: 251
       29.43 -    44.15: 54
       44.15 -    58.86: 4
       58.86 -    73.58: 6
  Dihedral angle restraints: 2846
    sinusoidal: 1082
      harmonic: 1764
  Sorted by residual:
  dihedral pdb=" CA  PRO A 364 "
           pdb=" C   PRO A 364 "
           pdb=" N   GLU A 365 "
           pdb=" CA  GLU A 365 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.02  -15.98     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CB  MET A 251 "
           pdb=" CG  MET A 251 "
           pdb=" SD  MET A 251 "
           pdb=" CE  MET A 251 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  106.33  -46.33     3      1.50e+01 4.44e-03 8.32e+00
  dihedral pdb=" CB  MET B 251 "
           pdb=" CG  MET B 251 "
           pdb=" SD  MET B 251 "
           pdb=" CE  MET B 251 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  106.19  -46.19     3      1.50e+01 4.44e-03 8.29e+00
  ... (remaining 2843 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 452
       0.024 -    0.049: 208
       0.049 -    0.073: 110
       0.073 -    0.098: 26
       0.098 -    0.122: 10
  Chirality restraints: 806
  Sorted by residual:
  chirality pdb=" CA  GLU A 281 "
            pdb=" N   GLU A 281 "
            pdb=" C   GLU A 281 "
            pdb=" CB  GLU A 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.73e-01
  chirality pdb=" CA  GLU B 281 "
            pdb=" N   GLU B 281 "
            pdb=" C   GLU B 281 "
            pdb=" CB  GLU B 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.62e-01
  chirality pdb=" CA  ILE B 319 "
            pdb=" N   ILE B 319 "
            pdb=" C   ILE B 319 "
            pdb=" CB  ILE B 319 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.24e-01
  ... (remaining 803 not shown)

  Planarity restraints: 784
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 365 "   -0.005 2.00e-02 2.50e+03   1.01e-02 1.02e+00
        pdb=" C   GLU A 365 "    0.017 2.00e-02 2.50e+03
        pdb=" O   GLU A 365 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   CYS A 366 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 363 "    0.016 5.00e-02 4.00e+02   2.35e-02 8.87e-01
        pdb=" N   PRO A 364 "   -0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO A 364 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 364 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 253 "    0.009 5.00e-02 4.00e+02   1.36e-02 2.97e-01
        pdb=" N   PRO B 254 "   -0.024 5.00e-02 4.00e+02
        pdb=" CA  PRO B 254 "    0.007 5.00e-02 4.00e+02
        pdb=" CD  PRO B 254 "    0.008 5.00e-02 4.00e+02
  ... (remaining 781 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 21
        2.60 -     3.18: 3955
        3.18 -     3.75: 6701
        3.75 -     4.33: 8672
        4.33 -     4.90: 14189
  Nonbonded interactions: 33538
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 357 "
            pdb="ZN    ZN B 401 "
     model   vdw
     2.030 2.230
  nonbonded pdb=" OE2 GLU A 357 "
            pdb="ZN    ZN A 402 "
     model   vdw
     2.033 2.230
  nonbonded pdb=" OG1 THR A 123 "
            pdb=" O   ARG A 125 "
     model   vdw
     2.376 3.040
  nonbonded pdb=" OG1 THR B 123 "
            pdb=" O   ARG B 125 "
     model   vdw
     2.380 3.040
  nonbonded pdb=" ND1 HIS B 323 "
            pdb=" OE2 GLU B 357 "
     model   vdw
     2.381 3.120
  ... (remaining 33533 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.980
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.370
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
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      :  0.002   0.018   4794  Z= 0.122
  Angle     :  0.392   6.520   6510  Z= 0.205
  Chirality :  0.036   0.122    806
  Planarity :  0.002   0.024    784
  Dihedral  : 12.510  73.577   1690
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  0.06 (0.33), residues: 584
  helix:  0.37 (0.26), residues: 374
  sheet: -1.33 (0.59), residues: 50
  loop :  0.13 (0.47), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 311 
 HIS   0.002   0.000   HIS B 323 
 PHE   0.004   0.001   PHE B  63 
 TYR   0.008   0.001   TYR A 289 
 ARG   0.001   0.000   ARG A 132 

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

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

  1168 Ramachandran restraints generated.
    584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1168 Ramachandran restraints generated.
    584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  180 LEU cc_start: 0.8354 (tp) cc_final: 0.7922 (tt)
REVERT: B  265 LEU cc_start: 0.8372 (mm) cc_final: 0.8023 (mp)
REVERT: A  180 LEU cc_start: 0.8406 (tp) cc_final: 0.7997 (tt)
REVERT: A  265 LEU cc_start: 0.8387 (mm) cc_final: 0.8040 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.2147
  time to fit residues: 23.1846
Evaluate side-chains
  61 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    0.5980
   chunk 45 optimal weight:    0.8980
   chunk 25 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 30 optimal weight:    8.9990
   chunk 24 optimal weight:    0.6980
   chunk 47 optimal weight:   10.0000
   chunk 18 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 35 optimal weight:    7.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B  49 ASN
A  49 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4798 r_free = 0.4798 target = 0.233398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.224578 restraints weight = 5442.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4699 r_free = 0.4699 target = 0.223457 restraints weight = 6765.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4677 r_free = 0.4677 target = 0.221205 restraints weight = 7124.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.4683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7169
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   4794  Z= 0.199
  Angle     :  0.525   5.300   6510  Z= 0.280
  Chirality :  0.039   0.126    806
  Planarity :  0.003   0.025    784
  Dihedral  :  3.760  17.074    630
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  :  9.47 %
    Favored  : 88.45 %
  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:  0.78 (0.35), residues: 584
  helix:  1.03 (0.27), residues: 384
  sheet: -1.21 (0.57), residues: 50
  loop :  0.08 (0.50), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 311 
 HIS   0.004   0.001   HIS A 306 
 PHE   0.008   0.001   PHE B 223 
 TYR   0.009   0.001   TYR B 289 
 ARG   0.003   0.000   ARG B  57 

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

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

  1168 Ramachandran restraints generated.
    584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1168 Ramachandran restraints generated.
    584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  265 LEU cc_start: 0.8469 (mm) cc_final: 0.8070 (mt)
REVERT: A  265 LEU cc_start: 0.8420 (mm) cc_final: 0.8018 (mt)
  outliers start: 11
  outliers final: 9
  residues processed: 74
  average time/residue: 0.1210
  time to fit residues: 12.6815
Evaluate side-chains
  64 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 CYS
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  245 PHE
Chi-restraints excluded: chain A residue   46 CYS
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  245 PHE
Chi-restraints excluded: chain A residue  353 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 43 optimal weight:    7.9990
   chunk 41 optimal weight:    0.0980
   chunk 36 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 47 optimal weight:    9.9990
   chunk 48 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.7384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.212415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.186806 restraints weight = 5578.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.183699 restraints weight = 11694.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.182526 restraints weight = 12481.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.4210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.2998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4794  Z= 0.179
  Angle     :  0.501   5.850   6510  Z= 0.262
  Chirality :  0.038   0.126    806
  Planarity :  0.003   0.026    784
  Dihedral  :  3.573  16.243    630
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 14.02 %
    Favored  : 84.09 %
  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:  0.87 (0.35), residues: 584
  helix:  1.17 (0.28), residues: 386
  sheet: -1.02 (0.63), residues: 50
  loop : -0.17 (0.48), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 311 
 HIS   0.003   0.001   HIS A 306 
 PHE   0.009   0.001   PHE B 245 
 TYR   0.011   0.001   TYR B 289 
 ARG   0.002   0.000   ARG A  57 

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

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

  1168 Ramachandran restraints generated.
    584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1168 Ramachandran restraints generated.
    584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  265 LEU cc_start: 0.8374 (mm) cc_final: 0.7972 (mt)
REVERT: B  315 MET cc_start: 0.7485 (tpp) cc_final: 0.6986 (tpp)
  outliers start: 10
  outliers final: 9
  residues processed: 68
  average time/residue: 0.1311
  time to fit residues: 12.5767
Evaluate side-chains
  69 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 CYS
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  245 PHE
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain A residue   46 CYS
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  353 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 17 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    1.5588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.206770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 210)---------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.175336 restraints weight = 5669.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 93)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.160411 restraints weight = 10087.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.161108 restraints weight = 7690.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.3165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4794  Z= 0.271
  Angle     :  0.540   5.454   6510  Z= 0.287
  Chirality :  0.040   0.145    806
  Planarity :  0.003   0.024    784
  Dihedral  :  3.964  16.771    630
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 14.39 %
    Favored  : 81.82 %
  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:  0.86 (0.35), residues: 584
  helix:  1.16 (0.28), residues: 386
  sheet: -1.27 (0.65), residues: 50
  loop : -0.06 (0.49), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 311 
 HIS   0.003   0.001   HIS A 225 
 PHE   0.018   0.001   PHE A  63 
 TYR   0.018   0.001   TYR B 289 
 ARG   0.002   0.000   ARG A  57 

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

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

  1168 Ramachandran restraints generated.
    584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1168 Ramachandran restraints generated.
    584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 58
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  251 MET cc_start: 0.7589 (pmm) cc_final: 0.6989 (pmm)
REVERT: A  172 MET cc_start: 0.6642 (pmm) cc_final: 0.6428 (pmm)
  outliers start: 20
  outliers final: 14
  residues processed: 69
  average time/residue: 0.1275
  time to fit residues: 12.3478
Evaluate side-chains
  70 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 CYS
Chi-restraints excluded: chain B residue   78 PHE
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain A residue   46 CYS
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  353 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 31 optimal weight:    0.1980
   chunk 21 optimal weight:    0.4980
   chunk 41 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 57 optimal weight:    0.4980
   chunk 33 optimal weight:    0.9980
   chunk 48 optimal weight:    8.9990
   chunk 12 optimal weight:    0.3980
   chunk 20 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.4780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.211341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.187210 restraints weight = 5661.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.169115 restraints weight = 8905.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.168834 restraints weight = 7669.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.4008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.3463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4794  Z= 0.158
  Angle     :  0.487   6.148   6510  Z= 0.258
  Chirality :  0.037   0.141    806
  Planarity :  0.002   0.023    784
  Dihedral  :  3.492  15.476    630
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 17.23 %
    Favored  : 80.30 %
  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:  1.22 (0.35), residues: 584
  helix:  1.49 (0.28), residues: 382
  sheet: -1.02 (0.65), residues: 50
  loop : -0.11 (0.47), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 311 
 HIS   0.003   0.001   HIS A 306 
 PHE   0.018   0.001   PHE A  63 
 TYR   0.012   0.001   TYR B 154 
 ARG   0.001   0.000   ARG A 125 

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

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

  1168 Ramachandran restraints generated.
    584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1168 Ramachandran restraints generated.
    584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.510 
Fit side-chains
REVERT: B  251 MET cc_start: 0.7523 (pmm) cc_final: 0.6973 (pmm)
REVERT: A  172 MET cc_start: 0.6526 (pmm) cc_final: 0.6315 (pmm)
  outliers start: 13
  outliers final: 11
  residues processed: 75
  average time/residue: 0.1162
  time to fit residues: 12.3956
Evaluate side-chains
  64 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 CYS
Chi-restraints excluded: chain B residue   78 PHE
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain A residue   46 CYS
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  227 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 34 optimal weight:    8.9990
   chunk 28 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 47 optimal weight:    0.2980
   chunk 31 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    1.0586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.209049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 129)---------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.167989 restraints weight = 5708.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.167690 restraints weight = 5822.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.167576 restraints weight = 6227.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.4000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.3536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4794  Z= 0.217
  Angle     :  0.517   6.324   6510  Z= 0.274
  Chirality :  0.038   0.155    806
  Planarity :  0.003   0.022    784
  Dihedral  :  3.718  15.270    630
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 17.80 %
    Favored  : 78.98 %
  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:  1.22 (0.35), residues: 584
  helix:  1.52 (0.28), residues: 382
  sheet: -1.06 (0.64), residues: 50
  loop : -0.17 (0.47), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 311 
 HIS   0.003   0.001   HIS A 306 
 PHE   0.025   0.002   PHE B 109 
 TYR   0.013   0.001   TYR B 289 
 ARG   0.001   0.000   ARG A  57 

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

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

  1168 Ramachandran restraints generated.
    584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1168 Ramachandran restraints generated.
    584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 52
  time to evaluate  : 0.495 
Fit side-chains
REVERT: B  251 MET cc_start: 0.7108 (pmm) cc_final: 0.6730 (pmm)
REVERT: A  172 MET cc_start: 0.6631 (pmm) cc_final: 0.6392 (pmm)
  outliers start: 17
  outliers final: 15
  residues processed: 64
  average time/residue: 0.1248
  time to fit residues: 11.2944
Evaluate side-chains
  67 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 52
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 CYS
Chi-restraints excluded: chain B residue   78 PHE
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain A residue   46 CYS
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  353 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0770
   chunk 58 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0970
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.5538

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.212125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 134)---------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.168902 restraints weight = 5668.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.167059 restraints weight = 6883.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.167178 restraints weight = 6659.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.3770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   4794  Z= 0.170
  Angle     :  0.503   6.815   6510  Z= 0.264
  Chirality :  0.037   0.137    806
  Planarity :  0.002   0.021    784
  Dihedral  :  3.429  14.509    630
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 17.23 %
    Favored  : 79.55 %
  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:  1.29 (0.35), residues: 584
  helix:  1.53 (0.27), residues: 390
  sheet: -0.88 (0.66), residues: 50
  loop : -0.19 (0.47), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 311 
 HIS   0.002   0.000   HIS A 306 
 PHE   0.020   0.001   PHE A  63 
 TYR   0.011   0.001   TYR B 154 
 ARG   0.001   0.000   ARG A 159 

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

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

  1168 Ramachandran restraints generated.
    584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1168 Ramachandran restraints generated.
    584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 52
  time to evaluate  : 0.518 
Fit side-chains
REVERT: B  251 MET cc_start: 0.7196 (pmm) cc_final: 0.6763 (pmm)
REVERT: B  275 LEU cc_start: 0.8445 (tt) cc_final: 0.8195 (tt)
REVERT: A  172 MET cc_start: 0.6641 (pmm) cc_final: 0.6380 (pmm)
REVERT: A  275 LEU cc_start: 0.8450 (tt) cc_final: 0.8219 (tt)
  outliers start: 17
  outliers final: 10
  residues processed: 66
  average time/residue: 0.1253
  time to fit residues: 11.6864
Evaluate side-chains
  60 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 CYS
Chi-restraints excluded: chain B residue   78 PHE
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain A residue   46 CYS
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  227 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 42 optimal weight:    9.9990
   chunk 14 optimal weight:    0.2980
   chunk 43 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.9986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.210428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.185633 restraints weight = 5616.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.164439 restraints weight = 9724.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.166126 restraints weight = 8465.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.3766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4794  Z= 0.219
  Angle     :  0.542   7.645   6510  Z= 0.282
  Chirality :  0.038   0.147    806
  Planarity :  0.003   0.021    784
  Dihedral  :  3.611  14.586    630
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 19.70 %
    Favored  : 77.65 %
  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:  1.37 (0.35), residues: 584
  helix:  1.66 (0.28), residues: 382
  sheet: -1.08 (0.63), residues: 50
  loop : -0.15 (0.48), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 130 
 HIS   0.003   0.001   HIS B 306 
 PHE   0.026   0.002   PHE B 109 
 TYR   0.013   0.001   TYR B 289 
 ARG   0.001   0.000   ARG A  57 

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

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

  1168 Ramachandran restraints generated.
    584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1168 Ramachandran restraints generated.
    584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.490 
Fit side-chains
REVERT: B  251 MET cc_start: 0.7492 (pmm) cc_final: 0.6937 (pmm)
REVERT: A  172 MET cc_start: 0.6451 (pmm) cc_final: 0.6208 (pmm)
  outliers start: 14
  outliers final: 11
  residues processed: 62
  average time/residue: 0.1236
  time to fit residues: 10.7678
Evaluate side-chains
  61 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 CYS
Chi-restraints excluded: chain B residue   78 PHE
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain A residue   46 CYS
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  353 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 34 optimal weight:    4.9990
   chunk 48 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 59 optimal weight:    0.2980
   chunk 16 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   overall best weight:    1.2384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.200431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 90)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.174689 restraints weight = 5766.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.174647 restraints weight = 8455.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.156022 restraints weight = 8199.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.3817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4794  Z= 0.249
  Angle     :  0.579   8.097   6510  Z= 0.303
  Chirality :  0.039   0.151    806
  Planarity :  0.003   0.020    784
  Dihedral  :  3.781  15.577    630
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 19.89 %
    Favored  : 77.65 %
  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:  1.35 (0.35), residues: 584
  helix:  1.63 (0.28), residues: 376
  sheet: -1.29 (0.62), residues: 50
  loop :  0.01 (0.48), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 130 
 HIS   0.003   0.001   HIS A 225 
 PHE   0.020   0.001   PHE A  63 
 TYR   0.015   0.001   TYR B 289 
 ARG   0.001   0.000   ARG A  57 

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

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

  1168 Ramachandran restraints generated.
    584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1168 Ramachandran restraints generated.
    584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 52
  time to evaluate  : 0.523 
Fit side-chains
REVERT: B  251 MET cc_start: 0.7471 (pmm) cc_final: 0.6944 (pmm)
REVERT: A  172 MET cc_start: 0.6592 (pmm) cc_final: 0.6391 (pmm)
  outliers start: 13
  outliers final: 13
  residues processed: 63
  average time/residue: 0.1289
  time to fit residues: 11.4059
Evaluate side-chains
  63 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 CYS
Chi-restraints excluded: chain B residue   78 PHE
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain A residue   46 CYS
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  353 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 41 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.9384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.202279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.176311 restraints weight = 5707.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.157505 restraints weight = 8787.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.157210 restraints weight = 9219.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.3868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4794  Z= 0.222
  Angle     :  0.573   9.113   6510  Z= 0.297
  Chirality :  0.038   0.145    806
  Planarity :  0.003   0.021    784
  Dihedral  :  3.663  14.914    630
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 19.51 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.35), residues: 584
  helix:  1.58 (0.27), residues: 382
  sheet: -1.43 (0.60), residues: 50
  loop : -0.23 (0.48), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 130 
 HIS   0.003   0.001   HIS A 306 
 PHE   0.027   0.002   PHE B 109 
 TYR   0.012   0.001   TYR B 289 
 ARG   0.001   0.000   ARG A  57 

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

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

  1168 Ramachandran restraints generated.
    584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1168 Ramachandran restraints generated.
    584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.554 
Fit side-chains
REVERT: B  251 MET cc_start: 0.7380 (pmm) cc_final: 0.6906 (pmm)
REVERT: A  172 MET cc_start: 0.6643 (pmm) cc_final: 0.6419 (pmm)
REVERT: A  365 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7418 (tm-30)
  outliers start: 13
  outliers final: 11
  residues processed: 61
  average time/residue: 0.1408
  time to fit residues: 12.1076
Evaluate side-chains
  62 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 CYS
Chi-restraints excluded: chain B residue   78 PHE
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain A residue   46 CYS
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  353 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 59 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 55 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.202652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 109)---------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.176457 restraints weight = 5765.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.158104 restraints weight = 8802.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.158289 restraints weight = 9282.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.3977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4794  Z= 0.210
  Angle     :  0.562   8.908   6510  Z= 0.291
  Chirality :  0.038   0.141    806
  Planarity :  0.002   0.021    784
  Dihedral  :  3.554  14.578    630
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 20.08 %
    Favored  : 78.03 %
  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:  1.40 (0.35), residues: 584
  helix:  1.72 (0.27), residues: 378
  sheet: -1.38 (0.61), residues: 50
  loop : -0.11 (0.48), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 130 
 HIS   0.003   0.001   HIS A 306 
 PHE   0.021   0.001   PHE A  63 
 TYR   0.011   0.001   TYR B 289 
 ARG   0.001   0.000   ARG B 159 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1654.17 seconds
wall clock time: 30 minutes 20.39 seconds (1820.39 seconds total)