Starting phenix.real_space_refine
on Tue May 13 19:13:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wbf_37423/05_2025/8wbf_37423_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wbf_37423/05_2025/8wbf_37423.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wbf_37423/05_2025/8wbf_37423.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wbf_37423/05_2025/8wbf_37423.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wbf_37423/05_2025/8wbf_37423_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wbf_37423/05_2025/8wbf_37423_neut.cif"
  }
  resolution = 2.99
  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=   0.137
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      80      5.16       5
     C    6852      2.51       5
     N    1958      2.21       5
     O    2024      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 10914
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 352, 2819
          Classifications: {'peptide': 352}
          Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332}
    Chain: "B"
      Number of atoms: 2819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 352, 2819
          Classifications: {'peptide': 352}
          Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332}
    Chain: "a"
      Number of atoms: 2638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2638
          Classifications: {'peptide': 330}
          Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 311}
          Chain breaks: 1
    Chain: "b"
      Number of atoms: 2638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2638
          Classifications: {'peptide': 330}
          Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 311}
          Chain breaks: 1
  Time building chain proxies: 6.95, per 1000 atoms: 0.64
  Number of scatterers: 10914
  At special positions: 0
  Unit cell: (114.75, 116.45, 110.5, 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      80     16.00
     O    2024      8.00
     N    1958      7.00
     C    6852      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=24, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   4 " - pdb=" SG  CYS A  15 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  55 " - pdb=" SG  CYS A 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 179 " - pdb=" SG  CYS A 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 280 " - pdb=" SG  CYS A 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 313 " - pdb=" SG  CYS A 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   4 " - pdb=" SG  CYS B  15 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  55 " - pdb=" SG  CYS B 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 179 " - pdb=" SG  CYS B 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 280 " - pdb=" SG  CYS B 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 313 " - pdb=" SG  CYS B 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a   4 " - pdb=" SG  CYS a  15 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a  55 " - pdb=" SG  CYS a 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a 179 " - pdb=" SG  CYS a 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a 280 " - pdb=" SG  CYS a 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a 291 " - pdb=" SG  CYS a 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a 313 " - pdb=" SG  CYS a 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b   4 " - pdb=" SG  CYS b  15 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b  55 " - pdb=" SG  CYS b 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b 179 " - pdb=" SG  CYS b 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b 280 " - pdb=" SG  CYS b 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b 291 " - pdb=" SG  CYS b 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b 313 " - pdb=" SG  CYS b 316 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.75
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2520

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 20 sheets defined
      18.7% alpha, 19.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 53
      removed outlier: 3.726A  pdb=" N   ALA A  43 " --> pdb=" O   PRO A  39 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ALA A  44 " --> pdb=" O   ARG A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 70
      removed outlier: 3.885A  pdb=" N   ASN A  65 " --> pdb=" O   SER A  61 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ILE A  66 " --> pdb=" O   ARG A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 82
    Processing helix  chain 'A' and resid 144 through 148
      removed outlier: 3.645A  pdb=" N   ARG A 148 " --> pdb=" O   LEU A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 3.512A  pdb=" N   THR A 230 " --> pdb=" O   LYS A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 248
      removed outlier: 3.538A  pdb=" N   ALA A 248 " --> pdb=" O   LYS A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 256
    Processing helix  chain 'A' and resid 341 through 345
    Processing helix  chain 'B' and resid 38 through 51
      removed outlier: 3.867A  pdb=" N   ALA B  43 " --> pdb=" O   PRO B  39 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLU B  51 " --> pdb=" O   LYS B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 82
      removed outlier: 3.630A  pdb=" N   ASN B  65 " --> pdb=" O   SER B  61 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  67 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   GLY B  73 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
      removed outlier: 5.642A  pdb=" N   GLU B  74 " --> pdb=" O   SER B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 146
      No H-bonds generated for 'chain 'B' and resid 144 through 146'
    Processing helix  chain 'B' and resid 180 through 183
      removed outlier: 4.059A  pdb=" N   VAL B 183 " --> pdb=" O   ASP B 180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 180 through 183'
    Processing helix  chain 'B' and resid 226 through 230
    Processing helix  chain 'B' and resid 237 through 241
      removed outlier: 3.864A  pdb=" N   LEU B 241 " --> pdb=" O   GLU B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 248
      removed outlier: 3.697A  pdb=" N   ALA B 248 " --> pdb=" O   LYS B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 256
      removed outlier: 3.534A  pdb=" N   THR B 256 " --> pdb=" O   HIS B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 341 through 345
      removed outlier: 3.697A  pdb=" N   ASN B 344 " --> pdb=" O   PRO B 341 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LEU B 345 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 341 through 345'
    Processing helix  chain 'a' and resid 38 through 53
    Processing helix  chain 'a' and resid 61 through 82
      removed outlier: 4.970A  pdb=" N   GLY a  73 " --> pdb=" O   ARG a  69 " (cutoff:3.500A)
      removed outlier: 5.088A  pdb=" N   GLU a  74 " --> pdb=" O   SER a  70 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASN a  82 " --> pdb=" O   ILE a  78 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 180 through 183
      removed outlier: 3.920A  pdb=" N   VAL a 183 " --> pdb=" O   ASP a 180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'a' and resid 180 through 183'
    Processing helix  chain 'a' and resid 226 through 230
    Processing helix  chain 'a' and resid 244 through 248
      removed outlier: 3.631A  pdb=" N   ALA a 248 " --> pdb=" O   LYS a 245 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 252 through 256
    Processing helix  chain 'a' and resid 341 through 345
      removed outlier: 3.527A  pdb=" N   ASN a 344 " --> pdb=" O   PRO a 341 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU a 345 " --> pdb=" O   GLU a 342 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'a' and resid 341 through 345'
    Processing helix  chain 'b' and resid 38 through 53
    Processing helix  chain 'b' and resid 61 through 82
      removed outlier: 4.835A  pdb=" N   GLY b  73 " --> pdb=" O   ARG b  69 " (cutoff:3.500A)
      removed outlier: 5.056A  pdb=" N   GLU b  74 " --> pdb=" O   SER b  70 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ASN b  82 " --> pdb=" O   ILE b  78 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 180 through 183
      removed outlier: 3.859A  pdb=" N   VAL b 183 " --> pdb=" O   ASP b 180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'b' and resid 180 through 183'
    Processing helix  chain 'b' and resid 226 through 230
    Processing helix  chain 'b' and resid 244 through 248
      removed outlier: 3.572A  pdb=" N   ALA b 248 " --> pdb=" O   LYS b 245 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 252 through 256
    Processing helix  chain 'b' and resid 341 through 345
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7
      removed outlier: 3.777A  pdb=" N   GLU a  12 " --> pdb=" O   ASP a   7 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   VAL a   2 " --> pdb=" O   VAL A   6 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 36
      removed outlier: 6.709A  pdb=" N   LYS A 170 " --> pdb=" O   VAL A 155 " (cutoff:3.500A)
      removed outlier: 5.522A  pdb=" N   VAL A 155 " --> pdb=" O   LYS A 170 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 57
      removed outlier: 6.519A  pdb=" N   THR A  87 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   VAL A 135 " --> pdb=" O   THR A  87 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   VAL A  89 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 331
      removed outlier: 4.700A  pdb=" N   PHE A 277 " --> pdb=" O   LYS A 213 " (cutoff:3.500A)
      removed outlier: 9.243A  pdb=" N   LYS A 213 " --> pdb=" O   PHE A 277 " (cutoff:3.500A)
      removed outlier: 5.583A  pdb=" N   LEU A 212 " --> pdb=" O   GLU A 205 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   GLU A 205 " --> pdb=" O   LEU A 212 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ARG A 214 " --> pdb=" O   GLU A 203 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ALA A 193 " --> pdb=" O   SER A 204 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   GLU a 192 " --> pdb=" O   LYS a 189 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA a 193 " --> pdb=" O   SER a 204 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ARG a 214 " --> pdb=" O   GLU a 203 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   GLU a 205 " --> pdb=" O   LEU a 212 " (cutoff:3.500A)
      removed outlier: 5.518A  pdb=" N   LEU a 212 " --> pdb=" O   GLU a 205 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ALA a 325 " --> pdb=" O   GLY a 328 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   GLY a 328 " --> pdb=" O   ALA a 325 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 287
      removed outlier: 6.235A  pdb=" N   LYS A 284 " --> pdb=" O   TRP A 311 " (cutoff:3.500A)
      removed outlier: 7.535A  pdb=" N   CYS A 313 " --> pdb=" O   LYS A 284 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   HIS A 286 " --> pdb=" O   CYS A 313 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 6
      removed outlier: 3.958A  pdb=" N   GLU b  12 " --> pdb=" O   ASP b   7 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   VAL b   2 " --> pdb=" O   VAL B   6 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 33 through 36
      removed outlier: 6.512A  pdb=" N   LYS B  33 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   LEU B 169 " --> pdb=" O   LYS B  33 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   HIS B  35 " --> pdb=" O   LEU B 169 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   VAL B 171 " --> pdb=" O   HIS B  35 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ASP B 157 " --> pdb=" O   TRP B 168 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   LYS B 170 " --> pdb=" O   VAL B 155 " (cutoff:3.500A)
      removed outlier: 5.294A  pdb=" N   VAL B 155 " --> pdb=" O   LYS B 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 56 through 57
      removed outlier: 6.800A  pdb=" N   GLY B  56 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 88 through 90
      removed outlier: 6.526A  pdb=" N   VAL B  89 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 329 through 331
      removed outlier: 4.565A  pdb=" N   PHE B 277 " --> pdb=" O   LYS B 213 " (cutoff:3.500A)
      removed outlier: 9.014A  pdb=" N   LYS B 213 " --> pdb=" O   PHE B 277 " (cutoff:3.500A)
      removed outlier: 5.449A  pdb=" N   LEU B 212 " --> pdb=" O   GLU B 205 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   GLU B 205 " --> pdb=" O   LEU B 212 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ALA B 193 " --> pdb=" O   SER B 204 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLU b 192 " --> pdb=" O   LYS b 189 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ARG b 214 " --> pdb=" O   GLU b 203 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   GLU b 205 " --> pdb=" O   LEU b 212 " (cutoff:3.500A)
      removed outlier: 5.352A  pdb=" N   LEU b 212 " --> pdb=" O   GLU b 205 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 284 through 287
      removed outlier: 6.231A  pdb=" N   LYS B 284 " --> pdb=" O   TRP B 311 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   CYS B 313 " --> pdb=" O   LYS B 284 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   HIS B 286 " --> pdb=" O   CYS B 313 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'a' and resid 35 through 36
      removed outlier: 7.155A  pdb=" N   HIS a  35 " --> pdb=" O   LEU a 169 " (cutoff:3.500A)
      removed outlier: 9.181A  pdb=" N   VAL a 171 " --> pdb=" O   HIS a  35 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'a' and resid 56 through 57
      removed outlier: 6.959A  pdb=" N   GLY a  56 " --> pdb=" O   ALA a 149 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'a' and resid 87 through 89
      removed outlier: 6.512A  pdb=" N   THR a  87 " --> pdb=" O   PHE a 133 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'a' and resid 284 through 287
      removed outlier: 6.130A  pdb=" N   LYS a 284 " --> pdb=" O   TRP a 311 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   CYS a 313 " --> pdb=" O   LYS a 284 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   HIS a 286 " --> pdb=" O   CYS a 313 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'b' and resid 35 through 36
      removed outlier: 6.787A  pdb=" N   HIS b  35 " --> pdb=" O   LEU b 169 " (cutoff:3.500A)
      removed outlier: 8.947A  pdb=" N   VAL b 171 " --> pdb=" O   HIS b  35 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'b' and resid 56 through 57
      removed outlier: 6.907A  pdb=" N   GLY b  56 " --> pdb=" O   ALA b 149 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'b' and resid 87 through 89
      removed outlier: 6.488A  pdb=" N   THR b  87 " --> pdb=" O   PHE b 133 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9
    Processing sheet with id=AC1, first strand: chain 'b' and resid 275 through 276
    Processing sheet with id=AC2, first strand: chain 'b' and resid 284 through 287
      removed outlier: 6.069A  pdb=" N   LYS b 284 " --> pdb=" O   TRP b 311 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   CYS b 313 " --> pdb=" O   LYS b 284 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   HIS b 286 " --> pdb=" O   CYS b 313 " (cutoff:3.500A)

    263 hydrogen bonds defined for protein.
    678 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: 3.08

  Time building geometry restraints manager: 3.18 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: 3627
        1.34 -     1.46: 2639
        1.46 -     1.58: 4830
        1.58 -     1.70: 0
        1.70 -     1.82: 112
  Bond restraints: 11208
  Sorted by residual:
  bond pdb=" N   LYS B 120 "
       pdb=" CA  LYS B 120 "
    ideal  model  delta    sigma   weight residual
    1.456  1.483 -0.027 1.22e-02 6.72e+03 4.81e+00
  bond pdb=" N   LYS A 120 "
       pdb=" CA  LYS A 120 "
    ideal  model  delta    sigma   weight residual
    1.456  1.480 -0.024 1.23e-02 6.61e+03 3.85e+00
  bond pdb=" CB  VAL B 188 "
       pdb=" CG2 VAL B 188 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.80e-01
  bond pdb=" CA  LYS A 120 "
       pdb=" C   LYS A 120 "
    ideal  model  delta    sigma   weight residual
    1.524  1.513  0.011 1.26e-02 6.30e+03 7.38e-01
  bond pdb=" CB  GLU B  12 "
       pdb=" CG  GLU B  12 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 6.82e-01
  ... (remaining 11203 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.97: 14325
        0.97 -     1.95: 687
        1.95 -     2.92: 132
        2.92 -     3.90: 34
        3.90 -     4.87: 14
  Bond angle restraints: 15192
  Sorted by residual:
  angle pdb=" N   GLY a 328 "
        pdb=" CA  GLY a 328 "
        pdb=" C   GLY a 328 "
      ideal   model   delta    sigma   weight residual
     110.43  115.30   -4.87 1.35e+00 5.49e-01 1.30e+01
  angle pdb=" CA  LYS B 120 "
        pdb=" C   LYS B 120 "
        pdb=" O   LYS B 120 "
      ideal   model   delta    sigma   weight residual
     120.81  117.82    2.99 1.15e+00 7.56e-01 6.78e+00
  angle pdb=" N   PRO B 144 "
        pdb=" CA  PRO B 144 "
        pdb=" C   PRO B 144 "
      ideal   model   delta    sigma   weight residual
     110.40  114.31   -3.91 1.61e+00 3.86e-01 5.91e+00
  angle pdb=" N   LYS A 120 "
        pdb=" CA  LYS A 120 "
        pdb=" CB  LYS A 120 "
      ideal   model   delta    sigma   weight residual
     109.83  113.36   -3.53 1.51e+00 4.39e-01 5.46e+00
  angle pdb=" C   ASP a 208 "
        pdb=" N   THR a 209 "
        pdb=" CA  THR a 209 "
      ideal   model   delta    sigma   weight residual
     121.80  125.79   -3.99 1.71e+00 3.42e-01 5.44e+00
  ... (remaining 15187 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.43: 6096
       17.43 -    34.86: 513
       34.86 -    52.28: 106
       52.28 -    69.71: 17
       69.71 -    87.14: 6
  Dihedral angle restraints: 6738
    sinusoidal: 2830
      harmonic: 3908
  Sorted by residual:
  dihedral pdb=" CB  CYS B 313 "
           pdb=" SG  CYS B 313 "
           pdb=" SG  CYS B 316 "
           pdb=" CB  CYS B 316 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -172.89   86.89     1      1.00e+01 1.00e-02 9.08e+01
  dihedral pdb=" CB  CYS a 313 "
           pdb=" SG  CYS a 313 "
           pdb=" SG  CYS a 316 "
           pdb=" CB  CYS a 316 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  172.27  -79.27     1      1.00e+01 1.00e-02 7.81e+01
  dihedral pdb=" CB  CYS b 313 "
           pdb=" SG  CYS b 313 "
           pdb=" SG  CYS b 316 "
           pdb=" CB  CYS b 316 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  165.47  -72.47     1      1.00e+01 1.00e-02 6.71e+01
  ... (remaining 6735 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 936
       0.028 -    0.056: 427
       0.056 -    0.084: 92
       0.084 -    0.112: 114
       0.112 -    0.141: 23
  Chirality restraints: 1592
  Sorted by residual:
  chirality pdb=" CB  THR a 209 "
            pdb=" CA  THR a 209 "
            pdb=" OG1 THR a 209 "
            pdb=" CG2 THR a 209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.14 2.00e-01 2.50e+01 4.94e-01
  chirality pdb=" CB  THR b 209 "
            pdb=" CA  THR b 209 "
            pdb=" OG1 THR b 209 "
            pdb=" CG2 THR b 209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.42    0.13 2.00e-01 2.50e+01 4.51e-01
  chirality pdb=" CA  ILE A  57 "
            pdb=" N   ILE A  57 "
            pdb=" C   ILE A  57 "
            pdb=" CB  ILE A  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.39e-01
  ... (remaining 1589 not shown)

  Planarity restraints: 1956
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 119 "   -0.006 2.00e-02 2.50e+03   1.26e-02 1.59e+00
        pdb=" C   GLY A 119 "    0.022 2.00e-02 2.50e+03
        pdb=" O   GLY A 119 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   LYS A 120 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 150 "   -0.009 2.00e-02 2.50e+03   7.86e-03 1.55e+00
        pdb=" CG  TRP A 150 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 150 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 150 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 150 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 150 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 150 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 150 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 150 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 150 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  71 "    0.006 2.00e-02 2.50e+03   1.22e-02 1.48e+00
        pdb=" C   VAL A  71 "   -0.021 2.00e-02 2.50e+03
        pdb=" O   VAL A  71 "    0.008 2.00e-02 2.50e+03
        pdb=" N   GLU A  72 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1953 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1466
        2.76 -     3.29: 9525
        3.29 -     3.83: 17133
        3.83 -     4.36: 20761
        4.36 -     4.90: 37488
  Nonbonded interactions: 86373
  Sorted by model distance:
  nonbonded pdb=" O   LEU b 231 "
            pdb=" OG  SER b 252 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   LEU a 231 "
            pdb=" OG  SER a 252 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OG  SER A 297 "
            pdb=" O   TYR A 331 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   GLY A 266 "
            pdb=" OG  SER A 348 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   MET b  97 "
            pdb=" OG1 THR b 222 "
     model   vdw
     2.255 3.040
  ... (remaining 86368 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: 0.03
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 107 or resid 130 through 352))
  selection = (chain 'B' and (resid 1 through 107 or resid 130 through 352))
  selection = 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.070
  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:             0.010
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     27.510
  Find NCS groups from input model:        0.490
  Set up NCS constraints:                  0.040
  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:10.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
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   0.031  11232  Z= 0.110
  Angle     :  0.510   4.870  15240  Z= 0.281
  Chirality :  0.042   0.141   1592
  Planarity :  0.003   0.027   1956
  Dihedral  : 13.353  87.141   4146
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.25 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -1.12 (0.23), residues: 1352
  helix:  1.86 (0.43), residues: 148
  sheet: -1.75 (0.31), residues: 302
  loop : -0.82 (0.21), residues: 902

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 150 
 HIS   0.006   0.001   HIS b 164 
 PHE   0.010   0.001   PHE B 277 
 TYR   0.009   0.001   TYR A 331 
 ARG   0.003   0.000   ARG a  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22813 (  263)
  hydrogen bonds       : angle       9.38571 (  678)
  SS BOND              : bond        0.00168 (   24)
  SS BOND              : angle       0.82015 (   48)
  covalent geometry    : bond        0.00232 (11208)
  covalent geometry    : angle       0.50857 (15192)

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 219
  time to evaluate  : 1.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 ASP cc_start: 0.7828 (t0) cc_final: 0.7511 (t70)
REVERT: A  261 ARG cc_start: 0.7795 (mtt90) cc_final: 0.7473 (mtp180)
REVERT: A  329 CYS cc_start: 0.7703 (t) cc_final: 0.7385 (t)
REVERT: B  103 ARG cc_start: 0.7620 (ptt90) cc_final: 0.7222 (ptt180)
REVERT: B  251 LEU cc_start: 0.8800 (mt) cc_final: 0.8536 (mt)
REVERT: B  286 HIS cc_start: 0.6971 (m170) cc_final: 0.6650 (m-70)
REVERT: a    7 ASP cc_start: 0.8067 (t0) cc_final: 0.7828 (t0)
REVERT: a   74 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6390 (tt0)
REVERT: a   82 ASN cc_start: 0.7339 (m110) cc_final: 0.7132 (m-40)
REVERT: a  213 LYS cc_start: 0.8889 (ttpt) cc_final: 0.8666 (tttt)
REVERT: a  258 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7517 (mt-10)
REVERT: a  274 GLU cc_start: 0.8772 (tt0) cc_final: 0.8469 (tt0)
REVERT: a  284 LYS cc_start: 0.7260 (mttt) cc_final: 0.6882 (mmmt)
REVERT: b   63 MET cc_start: 0.8131 (mmm) cc_final: 0.7777 (mmt)
REVERT: b   69 ARG cc_start: 0.7745 (ttm-80) cc_final: 0.7534 (mtt-85)
  outliers start: 1
  outliers final: 0
  residues processed: 220
  average time/residue: 1.3215
  time to fit residues: 311.6344
Evaluate side-chains
  150 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 1.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:   10.0000
   chunk 103 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 69 optimal weight:    8.9990
   chunk 55 optimal weight:    0.8980
   chunk 106 optimal weight:   10.0000
   chunk 41 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0070
   chunk 123 optimal weight:    2.9990
   overall best weight:    1.5804

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

Flipped N/Q/H residues before XYZ refinement:
A  76 ASN
A 158 HIS
A 254 HIS
B   1 HIS
B  95 ASN
B 131 ASN
B 207 ASN
B 254 HIS
a  35 HIS
a  48 GLN
a 195 HIS
a 216 HIS
a 254 HIS
a 255 ASN
a 286 HIS
b  35 HIS
b  48 GLN
b 254 HIS
b 255 ASN
b 286 HIS

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.159835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.124009 restraints weight = 11693.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.21
r_work: 0.3260 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.1542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093  11232  Z= 0.160
  Angle     :  0.589  15.224  15240  Z= 0.314
  Chirality :  0.044   0.193   1592
  Planarity :  0.004   0.044   1956
  Dihedral  :  4.496  19.248   1486
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  :  9.55 %
    Favored  : 87.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -1.01 (0.24), residues: 1352
  helix:  1.88 (0.42), residues: 152
  sheet: -1.59 (0.31), residues: 322
  loop : -0.74 (0.21), residues: 878

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 232 
 HIS   0.005   0.001   HIS b 164 
 PHE   0.014   0.001   PHE B 277 
 TYR   0.009   0.001   TYR A 122 
 ARG   0.005   0.000   ARG B 257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04372 (  263)
  hydrogen bonds       : angle       6.12273 (  678)
  SS BOND              : bond        0.00601 (   24)
  SS BOND              : angle       1.97805 (   48)
  covalent geometry    : bond        0.00394 (11208)
  covalent geometry    : angle       0.57913 (15192)

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 149
  time to evaluate  : 1.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 GLU cc_start: 0.5755 (tm-30) cc_final: 0.5359 (mt-10)
REVERT: A   85 GLN cc_start: 0.7981 (mt0) cc_final: 0.7243 (mm110)
REVERT: A  220 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.6994 (mpt)
REVERT: A  261 ARG cc_start: 0.8010 (mtt90) cc_final: 0.7466 (mtp180)
REVERT: A  263 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8028 (mt0)
REVERT: B  103 ARG cc_start: 0.7865 (ptt90) cc_final: 0.7475 (ptt180)
REVERT: B  286 HIS cc_start: 0.7040 (m170) cc_final: 0.6713 (m-70)
REVERT: B  340 GLU cc_start: 0.7674 (tp30) cc_final: 0.7404 (tp30)
REVERT: a   63 MET cc_start: 0.7896 (mmm) cc_final: 0.7566 (mpt)
REVERT: a   74 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6247 (tt0)
REVERT: a  224 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7628 (mt-10)
REVERT: a  255 ASN cc_start: 0.8853 (t0) cc_final: 0.8636 (t160)
REVERT: a  258 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7529 (mt-10)
REVERT: a  274 GLU cc_start: 0.8709 (tt0) cc_final: 0.8439 (tt0)
REVERT: a  278 GLU cc_start: 0.6826 (mt-10) cc_final: 0.6361 (pt0)
REVERT: a  284 LYS cc_start: 0.7188 (mttt) cc_final: 0.6707 (mmmt)
REVERT: b   11 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.6640 (mmtt)
REVERT: b  349 MET cc_start: 0.7309 (mmt) cc_final: 0.7026 (mmm)
  outliers start: 41
  outliers final: 18
  residues processed: 173
  average time/residue: 1.2737
  time to fit residues: 237.2588
Evaluate side-chains
  159 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 137
  time to evaluate  : 1.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  220 MET
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain B residue   30 ASP
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain a residue   13 THR
Chi-restraints excluded: chain a residue  106 VAL
Chi-restraints excluded: chain a residue  220 MET
Chi-restraints excluded: chain a residue  224 GLU
Chi-restraints excluded: chain a residue  279 GLU
Chi-restraints excluded: chain b residue    2 VAL
Chi-restraints excluded: chain b residue   11 LYS
Chi-restraints excluded: chain b residue   13 THR
Chi-restraints excluded: chain b residue   67 MET
Chi-restraints excluded: chain b residue  232 TRP
Chi-restraints excluded: chain b residue  287 VAL
Chi-restraints excluded: chain b residue  351 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 106 optimal weight:   10.0000
   chunk 134 optimal weight:    7.9990
   chunk 3 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 54 optimal weight:    0.6980
   chunk 114 optimal weight:   10.0000
   chunk 12 optimal weight:    7.9990
   chunk 50 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 130 optimal weight:    4.9990
   overall best weight:    3.5388

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

Flipped N/Q/H residues before XYZ refinement:
B 113 HIS
a  82 ASN
a 254 HIS
b 147 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.153134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.116578 restraints weight = 11949.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 2.22
r_work: 0.3154 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068  11232  Z= 0.278
  Angle     :  0.763  21.579  15240  Z= 0.397
  Chirality :  0.049   0.244   1592
  Planarity :  0.005   0.051   1956
  Dihedral  :  5.161  23.815   1486
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.02 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 14.07 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.23), residues: 1352
  helix:  1.56 (0.41), residues: 152
  sheet: -1.73 (0.30), residues: 316
  loop : -1.10 (0.21), residues: 884

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP B 232 
 HIS   0.006   0.002   HIS B 254 
 PHE   0.011   0.002   PHE a 323 
 TYR   0.021   0.002   TYR B 331 
 ARG   0.008   0.001   ARG b 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05148 (  263)
  hydrogen bonds       : angle       6.13215 (  678)
  SS BOND              : bond        0.00829 (   24)
  SS BOND              : angle       3.30607 (   48)
  covalent geometry    : bond        0.00687 (11208)
  covalent geometry    : angle       0.74155 (15192)

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 138
  time to evaluate  : 1.235 
Fit side-chains
REVERT: A   15 CYS cc_start: 0.6727 (OUTLIER) cc_final: 0.6209 (t)
REVERT: A  263 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8139 (mt0)
REVERT: A  342 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7502 (mp0)
REVERT: B  103 ARG cc_start: 0.7977 (ptt90) cc_final: 0.7553 (ptt180)
REVERT: B  136 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6885 (m-30)
REVERT: B  263 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.7403 (mp10)
REVERT: B  274 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8429 (tt0)
REVERT: B  340 GLU cc_start: 0.7757 (tp30) cc_final: 0.7418 (tp30)
REVERT: a   63 MET cc_start: 0.7969 (mmm) cc_final: 0.7281 (mpt)
REVERT: a   74 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6233 (tt0)
REVERT: a  224 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7006 (mt-10)
REVERT: a  258 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7530 (mt-10)
REVERT: a  274 GLU cc_start: 0.8773 (tt0) cc_final: 0.8495 (tt0)
REVERT: a  278 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6380 (pt0)
REVERT: a  284 LYS cc_start: 0.7138 (mttt) cc_final: 0.6648 (mmmt)
REVERT: b   11 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.6632 (mmtt)
REVERT: b   63 MET cc_start: 0.7420 (mmt) cc_final: 0.6757 (mmt)
REVERT: b  220 MET cc_start: 0.8156 (mpt) cc_final: 0.7684 (mpt)
  outliers start: 49
  outliers final: 25
  residues processed: 174
  average time/residue: 1.2613
  time to fit residues: 237.0787
Evaluate side-chains
  161 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 128
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue   15 CYS
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   80 GLU
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  136 ASP
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain B residue   30 ASP
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  263 GLN
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain a residue   13 THR
Chi-restraints excluded: chain a residue  106 VAL
Chi-restraints excluded: chain a residue  140 LEU
Chi-restraints excluded: chain a residue  173 GLU
Chi-restraints excluded: chain a residue  220 MET
Chi-restraints excluded: chain a residue  224 GLU
Chi-restraints excluded: chain a residue  279 GLU
Chi-restraints excluded: chain b residue    2 VAL
Chi-restraints excluded: chain b residue   11 LYS
Chi-restraints excluded: chain b residue   13 THR
Chi-restraints excluded: chain b residue   97 MET
Chi-restraints excluded: chain b residue  287 VAL
Chi-restraints excluded: chain b residue  351 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 47 optimal weight:    9.9990
   chunk 73 optimal weight:   10.0000
   chunk 118 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 31 optimal weight:    0.1980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 147 HIS
B 195 HIS
a 254 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.158802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.121669 restraints weight = 11733.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 2.31
r_work: 0.3233 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  11232  Z= 0.110
  Angle     :  0.584  15.102  15240  Z= 0.307
  Chirality :  0.042   0.216   1592
  Planarity :  0.004   0.040   1956
  Dihedral  :  4.523  21.267   1486
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 16.58 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -1.10 (0.23), residues: 1352
  helix:  2.03 (0.41), residues: 152
  sheet: -1.54 (0.32), residues: 304
  loop : -0.93 (0.21), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP b 232 
 HIS   0.004   0.001   HIS b 164 
 PHE   0.011   0.001   PHE B 277 
 TYR   0.015   0.001   TYR A 122 
 ARG   0.009   0.000   ARG b 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03384 (  263)
  hydrogen bonds       : angle       5.52064 (  678)
  SS BOND              : bond        0.00523 (   24)
  SS BOND              : angle       2.78417 (   48)
  covalent geometry    : bond        0.00255 (11208)
  covalent geometry    : angle       0.56403 (15192)

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 144
  time to evaluate  : 1.160 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.5863 (tm-30) cc_final: 0.5107 (tt0)
REVERT: A  258 GLU cc_start: 0.6964 (pm20) cc_final: 0.6759 (pm20)
REVERT: A  263 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.7928 (mt0)
REVERT: A  342 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7465 (mp0)
REVERT: B  103 ARG cc_start: 0.7859 (ptt90) cc_final: 0.7474 (ptt180)
REVERT: B  274 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8320 (tt0)
REVERT: B  286 HIS cc_start: 0.6936 (m170) cc_final: 0.6623 (m-70)
REVERT: a   63 MET cc_start: 0.7839 (mmm) cc_final: 0.7288 (mpt)
REVERT: a   74 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6187 (tt0)
REVERT: a  224 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.6893 (mt-10)
REVERT: a  258 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7557 (mt-10)
REVERT: a  274 GLU cc_start: 0.8738 (tt0) cc_final: 0.8531 (tt0)
REVERT: a  284 LYS cc_start: 0.7079 (mttt) cc_final: 0.6609 (mmmt)
REVERT: b   63 MET cc_start: 0.7469 (mmt) cc_final: 0.6730 (mmt)
REVERT: b   97 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7462 (mtt)
REVERT: b  314 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6827 (ttp-170)
REVERT: b  316 CYS cc_start: 0.6655 (m) cc_final: 0.6342 (m)
  outliers start: 34
  outliers final: 13
  residues processed: 165
  average time/residue: 1.2100
  time to fit residues: 215.1606
Evaluate side-chains
  155 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue   15 CYS
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain B residue   30 ASP
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain a residue   87 THR
Chi-restraints excluded: chain a residue  106 VAL
Chi-restraints excluded: chain a residue  220 MET
Chi-restraints excluded: chain a residue  224 GLU
Chi-restraints excluded: chain a residue  279 GLU
Chi-restraints excluded: chain b residue   97 MET
Chi-restraints excluded: chain b residue  314 ARG
Chi-restraints excluded: chain b residue  351 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 133 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   chunk 79 optimal weight:    6.9990
   chunk 35 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 83 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 118 optimal weight:    2.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** a  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
a 254 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.155796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.117740 restraints weight = 11731.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 2.45
r_work: 0.3185 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  11232  Z= 0.200
  Angle     :  0.673  18.318  15240  Z= 0.352
  Chirality :  0.045   0.204   1592
  Planarity :  0.004   0.041   1956
  Dihedral  :  4.794  22.248   1486
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.58 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 17.09 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -1.24 (0.23), residues: 1352
  helix:  2.04 (0.42), residues: 152
  sheet: -1.65 (0.33), residues: 282
  loop : -1.08 (0.20), residues: 918

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP b 232 
 HIS   0.006   0.001   HIS a 254 
 PHE   0.010   0.002   PHE a 323 
 TYR   0.015   0.002   TYR A 122 
 ARG   0.008   0.001   ARG b 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03982 (  263)
  hydrogen bonds       : angle       5.64465 (  678)
  SS BOND              : bond        0.00527 (   24)
  SS BOND              : angle       3.02742 (   48)
  covalent geometry    : bond        0.00494 (11208)
  covalent geometry    : angle       0.65179 (15192)

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 134
  time to evaluate  : 1.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 GLU cc_start: 0.5907 (tm-30) cc_final: 0.5370 (tt0)
REVERT: A  263 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8088 (mt0)
REVERT: A  342 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7545 (mp0)
REVERT: B  103 ARG cc_start: 0.8062 (ptt90) cc_final: 0.7688 (ptt180)
REVERT: B  274 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8401 (tt0)
REVERT: B  339 LYS cc_start: 0.7706 (tttp) cc_final: 0.7477 (mttt)
REVERT: B  340 GLU cc_start: 0.7827 (tp30) cc_final: 0.7564 (tp30)
REVERT: a   63 MET cc_start: 0.8034 (mmm) cc_final: 0.7308 (mpt)
REVERT: a   74 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6325 (tt0)
REVERT: a  224 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7939 (mt-10)
REVERT: a  258 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7510 (mt-10)
REVERT: a  274 GLU cc_start: 0.8843 (tt0) cc_final: 0.8623 (tt0)
REVERT: a  284 LYS cc_start: 0.7188 (mttt) cc_final: 0.6764 (mmmt)
REVERT: b  178 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7162 (mm-30)
REVERT: b  314 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.7085 (ttp-170)
  outliers start: 43
  outliers final: 27
  residues processed: 163
  average time/residue: 1.3310
  time to fit residues: 233.2344
Evaluate side-chains
  162 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 129
  time to evaluate  : 1.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue   15 CYS
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  136 ASP
Chi-restraints excluded: chain A residue  234 ASP
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain B residue   30 ASP
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain a residue   13 THR
Chi-restraints excluded: chain a residue   87 THR
Chi-restraints excluded: chain a residue   89 VAL
Chi-restraints excluded: chain a residue  106 VAL
Chi-restraints excluded: chain a residue  220 MET
Chi-restraints excluded: chain a residue  224 GLU
Chi-restraints excluded: chain a residue  279 GLU
Chi-restraints excluded: chain b residue    2 VAL
Chi-restraints excluded: chain b residue   13 THR
Chi-restraints excluded: chain b residue   51 GLU
Chi-restraints excluded: chain b residue   97 MET
Chi-restraints excluded: chain b residue  178 GLU
Chi-restraints excluded: chain b residue  287 VAL
Chi-restraints excluded: chain b residue  314 ARG
Chi-restraints excluded: chain b residue  351 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 99 optimal weight:   10.0000
   chunk 96 optimal weight:    6.9990
   chunk 77 optimal weight:    9.9990
   chunk 76 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
a  95 ASN
a 254 HIS
b 164 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.155296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.118485 restraints weight = 11827.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 2.28
r_work: 0.3169 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3016 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  11232  Z= 0.171
  Angle     :  0.647  17.220  15240  Z= 0.338
  Chirality :  0.044   0.220   1592
  Planarity :  0.004   0.047   1956
  Dihedral  :  4.753  22.307   1486
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 18.01 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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 (0.23), residues: 1352
  helix:  2.07 (0.42), residues: 152
  sheet: -1.55 (0.33), residues: 276
  loop : -1.10 (0.20), residues: 924

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP a  28 
 HIS   0.005   0.001   HIS B 254 
 PHE   0.010   0.001   PHE B 277 
 TYR   0.016   0.001   TYR b  34 
 ARG   0.009   0.001   ARG b 347 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03763 (  263)
  hydrogen bonds       : angle       5.56296 (  678)
  SS BOND              : bond        0.00483 (   24)
  SS BOND              : angle       2.90410 (   48)
  covalent geometry    : bond        0.00420 (11208)
  covalent geometry    : angle       0.62662 (15192)

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 140
  time to evaluate  : 1.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6965 (tt0)
REVERT: A  263 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8044 (mt0)
REVERT: A  342 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7575 (mp0)
REVERT: B  103 ARG cc_start: 0.7964 (ptt90) cc_final: 0.7558 (ptt180)
REVERT: B  263 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.7457 (mp10)
REVERT: B  274 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8368 (tt0)
REVERT: B  340 GLU cc_start: 0.7713 (tp30) cc_final: 0.7340 (tp30)
REVERT: a   63 MET cc_start: 0.7917 (mmm) cc_final: 0.7700 (mpt)
REVERT: a   74 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6207 (tt0)
REVERT: a  224 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7726 (mt-10)
REVERT: a  258 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7431 (mt-10)
REVERT: a  274 GLU cc_start: 0.8796 (tt0) cc_final: 0.8585 (tt0)
REVERT: a  284 LYS cc_start: 0.7021 (mttt) cc_final: 0.6487 (mmmt)
REVERT: b  178 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7001 (mm-30)
REVERT: b  314 ARG cc_start: 0.7205 (ttp-170) cc_final: 0.7003 (ttp-170)
  outliers start: 48
  outliers final: 30
  residues processed: 175
  average time/residue: 1.2360
  time to fit residues: 232.6146
Evaluate side-chains
  168 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 131
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue   15 CYS
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   80 GLU
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain B residue   30 ASP
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  263 GLN
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain a residue   13 THR
Chi-restraints excluded: chain a residue   87 THR
Chi-restraints excluded: chain a residue  106 VAL
Chi-restraints excluded: chain a residue  220 MET
Chi-restraints excluded: chain a residue  224 GLU
Chi-restraints excluded: chain a residue  279 GLU
Chi-restraints excluded: chain b residue    2 VAL
Chi-restraints excluded: chain b residue   13 THR
Chi-restraints excluded: chain b residue   51 GLU
Chi-restraints excluded: chain b residue   67 MET
Chi-restraints excluded: chain b residue   97 MET
Chi-restraints excluded: chain b residue  162 VAL
Chi-restraints excluded: chain b residue  178 GLU
Chi-restraints excluded: chain b residue  209 THR
Chi-restraints excluded: chain b residue  228 SER
Chi-restraints excluded: chain b residue  287 VAL
Chi-restraints excluded: chain b residue  351 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 104 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 81 optimal weight:    9.9990
   chunk 83 optimal weight:    5.9990
   chunk 92 optimal weight:    2.9990
   chunk 111 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9990
   chunk 110 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 34 optimal weight:    4.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
a 254 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.155135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.118245 restraints weight = 11915.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.29
r_work: 0.3168 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  11232  Z= 0.173
  Angle     :  0.655  17.204  15240  Z= 0.343
  Chirality :  0.044   0.209   1592
  Planarity :  0.004   0.041   1956
  Dihedral  :  4.752  22.244   1486
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.28 %
    Favored  : 91.72 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 18.09 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -1.23 (0.23), residues: 1352
  helix:  2.09 (0.42), residues: 152
  sheet: -1.65 (0.33), residues: 282
  loop : -1.07 (0.20), residues: 918

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP a  28 
 HIS   0.005   0.001   HIS B 254 
 PHE   0.010   0.001   PHE a 323 
 TYR   0.019   0.001   TYR A 122 
 ARG   0.009   0.000   ARG b 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03730 (  263)
  hydrogen bonds       : angle       5.52761 (  678)
  SS BOND              : bond        0.00483 (   24)
  SS BOND              : angle       2.93466 (   48)
  covalent geometry    : bond        0.00424 (11208)
  covalent geometry    : angle       0.63466 (15192)

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 135
  time to evaluate  : 1.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 GLU cc_start: 0.6110 (tm-30) cc_final: 0.5163 (tt0)
REVERT: A   80 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6906 (tt0)
REVERT: A  263 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8051 (mt0)
REVERT: A  342 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7549 (mp0)
REVERT: B  103 ARG cc_start: 0.7966 (ptt90) cc_final: 0.7552 (ptt180)
REVERT: B  263 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.7461 (mp10)
REVERT: B  274 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8377 (tt0)
REVERT: B  340 GLU cc_start: 0.7717 (tp30) cc_final: 0.7407 (tp30)
REVERT: a   63 MET cc_start: 0.7937 (mmm) cc_final: 0.7708 (mpt)
REVERT: a   74 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6230 (tt0)
REVERT: a  224 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7702 (mt-10)
REVERT: a  258 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7425 (mt-10)
REVERT: a  274 GLU cc_start: 0.8793 (tt0) cc_final: 0.8563 (tt0)
REVERT: a  284 LYS cc_start: 0.6970 (mttt) cc_final: 0.6435 (mmmt)
REVERT: b   11 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6625 (mmtt)
REVERT: b   63 MET cc_start: 0.8098 (mpp) cc_final: 0.7883 (mmt)
REVERT: b  178 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.6987 (mm-30)
REVERT: b  279 GLU cc_start: 0.7339 (pt0) cc_final: 0.6880 (pt0)
REVERT: b  314 ARG cc_start: 0.7177 (ttp-170) cc_final: 0.6921 (ttp-170)
  outliers start: 48
  outliers final: 32
  residues processed: 167
  average time/residue: 1.2565
  time to fit residues: 225.9971
Evaluate side-chains
  169 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 129
  time to evaluate  : 1.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue   15 CYS
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   80 GLU
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain B residue   30 ASP
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  263 GLN
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain a residue   13 THR
Chi-restraints excluded: chain a residue   87 THR
Chi-restraints excluded: chain a residue   89 VAL
Chi-restraints excluded: chain a residue  106 VAL
Chi-restraints excluded: chain a residue  220 MET
Chi-restraints excluded: chain a residue  224 GLU
Chi-restraints excluded: chain a residue  279 GLU
Chi-restraints excluded: chain b residue    2 VAL
Chi-restraints excluded: chain b residue   11 LYS
Chi-restraints excluded: chain b residue   13 THR
Chi-restraints excluded: chain b residue   51 GLU
Chi-restraints excluded: chain b residue   67 MET
Chi-restraints excluded: chain b residue   97 MET
Chi-restraints excluded: chain b residue  162 VAL
Chi-restraints excluded: chain b residue  178 GLU
Chi-restraints excluded: chain b residue  228 SER
Chi-restraints excluded: chain b residue  287 VAL
Chi-restraints excluded: chain b residue  351 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 78 optimal weight:    8.9990
   chunk 27 optimal weight:    3.9990
   chunk 2 optimal weight:    0.3980
   chunk 135 optimal weight:    0.8980
   chunk 117 optimal weight:    5.9990
   chunk 114 optimal weight:    2.9990
   chunk 129 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 147 HIS
a 254 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.157130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.120496 restraints weight = 11678.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 2.27
r_work: 0.3198 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  11232  Z= 0.130
  Angle     :  0.607  15.384  15240  Z= 0.319
  Chirality :  0.043   0.197   1592
  Planarity :  0.004   0.049   1956
  Dihedral  :  4.528  21.707   1486
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 19.35 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.23), residues: 1352
  helix:  2.18 (0.42), residues: 154
  sheet: -1.47 (0.32), residues: 304
  loop : -0.92 (0.21), residues: 894

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP a  28 
 HIS   0.004   0.001   HIS a 254 
 PHE   0.011   0.001   PHE B 277 
 TYR   0.016   0.001   TYR A 122 
 ARG   0.012   0.000   ARG b 347 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03319 (  263)
  hydrogen bonds       : angle       5.37084 (  678)
  SS BOND              : bond        0.00419 (   24)
  SS BOND              : angle       2.75526 (   48)
  covalent geometry    : bond        0.00316 (11208)
  covalent geometry    : angle       0.58818 (15192)

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 135
  time to evaluate  : 1.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 GLU cc_start: 0.5793 (tm-30) cc_final: 0.5108 (tt0)
REVERT: A   85 GLN cc_start: 0.7933 (mt0) cc_final: 0.7316 (mm110)
REVERT: A  263 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.7972 (mt0)
REVERT: A  342 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7501 (mp0)
REVERT: B  103 ARG cc_start: 0.7891 (ptt90) cc_final: 0.7475 (ptt180)
REVERT: B  274 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8296 (tt0)
REVERT: B  340 GLU cc_start: 0.7631 (tp30) cc_final: 0.7392 (tp30)
REVERT: a   63 MET cc_start: 0.7877 (mmm) cc_final: 0.7016 (mpt)
REVERT: a   74 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6163 (tt0)
REVERT: a  224 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7625 (mt-10)
REVERT: a  258 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7372 (mt-10)
REVERT: a  274 GLU cc_start: 0.8766 (tt0) cc_final: 0.8518 (tt0)
REVERT: a  284 LYS cc_start: 0.7015 (mttt) cc_final: 0.6465 (mmmt)
REVERT: b  314 ARG cc_start: 0.7134 (ttp-170) cc_final: 0.6912 (ttp-170)
  outliers start: 37
  outliers final: 27
  residues processed: 158
  average time/residue: 1.2693
  time to fit residues: 218.5714
Evaluate side-chains
  162 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 131
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue   15 CYS
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain B residue   30 ASP
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain a residue   13 THR
Chi-restraints excluded: chain a residue   89 VAL
Chi-restraints excluded: chain a residue  106 VAL
Chi-restraints excluded: chain a residue  220 MET
Chi-restraints excluded: chain a residue  224 GLU
Chi-restraints excluded: chain a residue  279 GLU
Chi-restraints excluded: chain b residue    2 VAL
Chi-restraints excluded: chain b residue   13 THR
Chi-restraints excluded: chain b residue   51 GLU
Chi-restraints excluded: chain b residue   67 MET
Chi-restraints excluded: chain b residue   97 MET
Chi-restraints excluded: chain b residue  162 VAL
Chi-restraints excluded: chain b residue  209 THR
Chi-restraints excluded: chain b residue  287 VAL
Chi-restraints excluded: chain b residue  351 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 105 optimal weight:    0.6980
   chunk 55 optimal weight:    4.9990
   chunk 118 optimal weight:    0.4980
   chunk 110 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 63 optimal weight:    7.9990
   chunk 96 optimal weight:    8.9990
   chunk 81 optimal weight:   10.0000
   chunk 82 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
a  95 ASN
a 254 HIS

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 = 0.156369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.119496 restraints weight = 11821.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 2.26
r_work: 0.3195 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.2425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  11232  Z= 0.151
  Angle     :  0.646  16.328  15240  Z= 0.337
  Chirality :  0.044   0.249   1592
  Planarity :  0.004   0.054   1956
  Dihedral  :  4.603  21.908   1486
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 19.10 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -1.06 (0.23), residues: 1352
  helix:  2.22 (0.42), residues: 154
  sheet: -1.56 (0.31), residues: 306
  loop : -0.92 (0.21), residues: 892

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP a  28 
 HIS   0.004   0.001   HIS B 254 
 PHE   0.010   0.001   PHE B 277 
 TYR   0.015   0.001   TYR A 122 
 ARG   0.011   0.000   ARG b 347 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03528 (  263)
  hydrogen bonds       : angle       5.39418 (  678)
  SS BOND              : bond        0.00527 (   24)
  SS BOND              : angle       3.07059 (   48)
  covalent geometry    : bond        0.00365 (11208)
  covalent geometry    : angle       0.62320 (15192)

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 144
  time to evaluate  : 1.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 GLU cc_start: 0.5787 (tm-30) cc_final: 0.5152 (tt0)
REVERT: A   80 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6940 (tt0)
REVERT: A   85 GLN cc_start: 0.7942 (mt0) cc_final: 0.7339 (mm110)
REVERT: A  263 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8015 (mt0)
REVERT: A  342 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7538 (mp0)
REVERT: B  103 ARG cc_start: 0.7922 (ptt90) cc_final: 0.7480 (ptt180)
REVERT: B  274 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8346 (tt0)
REVERT: B  340 GLU cc_start: 0.7661 (tp30) cc_final: 0.7420 (tp30)
REVERT: a   63 MET cc_start: 0.7943 (mmm) cc_final: 0.7001 (mpt)
REVERT: a   74 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6195 (tt0)
REVERT: a  224 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7729 (mt-10)
REVERT: a  258 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7411 (mt-10)
REVERT: a  274 GLU cc_start: 0.8780 (tt0) cc_final: 0.8562 (tt0)
REVERT: a  284 LYS cc_start: 0.7052 (mttt) cc_final: 0.6522 (mmmt)
REVERT: b  349 MET cc_start: 0.7292 (mmt) cc_final: 0.7088 (mmm)
  outliers start: 40
  outliers final: 28
  residues processed: 170
  average time/residue: 1.1811
  time to fit residues: 216.8959
Evaluate side-chains
  164 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 131
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue   15 CYS
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   80 GLU
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain B residue   30 ASP
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain a residue   13 THR
Chi-restraints excluded: chain a residue   87 THR
Chi-restraints excluded: chain a residue   89 VAL
Chi-restraints excluded: chain a residue  106 VAL
Chi-restraints excluded: chain a residue  220 MET
Chi-restraints excluded: chain a residue  224 GLU
Chi-restraints excluded: chain a residue  279 GLU
Chi-restraints excluded: chain b residue    2 VAL
Chi-restraints excluded: chain b residue   13 THR
Chi-restraints excluded: chain b residue   51 GLU
Chi-restraints excluded: chain b residue   97 MET
Chi-restraints excluded: chain b residue  162 VAL
Chi-restraints excluded: chain b residue  209 THR
Chi-restraints excluded: chain b residue  287 VAL
Chi-restraints excluded: chain b residue  351 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 18 optimal weight:    0.7980
   chunk 104 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 48 optimal weight:    8.9990
   chunk 74 optimal weight:    7.9990
   chunk 59 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
a  95 ASN
a 254 HIS

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 = 0.156381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.119630 restraints weight = 11732.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 2.25
r_work: 0.3188 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  11232  Z= 0.146
  Angle     :  0.713  26.414  15240  Z= 0.364
  Chirality :  0.044   0.281   1592
  Planarity :  0.004   0.061   1956
  Dihedral  :  4.588  21.896   1486
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 19.43 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -1.02 (0.23), residues: 1352
  helix:  2.24 (0.42), residues: 154
  sheet: -1.44 (0.32), residues: 300
  loop : -0.94 (0.21), residues: 898

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP a  28 
 HIS   0.004   0.001   HIS a 254 
 PHE   0.010   0.001   PHE B 277 
 TYR   0.015   0.001   TYR A 122 
 ARG   0.013   0.000   ARG b 347 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03674 (  263)
  hydrogen bonds       : angle       5.40984 (  678)
  SS BOND              : bond        0.00611 (   24)
  SS BOND              : angle       3.79927 (   48)
  covalent geometry    : bond        0.00351 (11208)
  covalent geometry    : angle       0.68104 (15192)

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 132
  time to evaluate  : 1.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 GLU cc_start: 0.5702 (tm-30) cc_final: 0.5067 (tt0)
REVERT: A   80 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6914 (tt0)
REVERT: A   85 GLN cc_start: 0.7931 (mt0) cc_final: 0.7312 (mm110)
REVERT: A  263 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8005 (mt0)
REVERT: A  342 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7566 (mp0)
REVERT: B  103 ARG cc_start: 0.7892 (ptt90) cc_final: 0.7449 (ptt180)
REVERT: B  217 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8420 (mt)
REVERT: B  274 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8338 (tt0)
REVERT: B  340 GLU cc_start: 0.7642 (tp30) cc_final: 0.7434 (tp30)
REVERT: a   63 MET cc_start: 0.7905 (mmm) cc_final: 0.6975 (mpt)
REVERT: a   74 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6133 (tt0)
REVERT: a  224 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7669 (mt-10)
REVERT: a  258 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7381 (mt-10)
REVERT: a  274 GLU cc_start: 0.8764 (tt0) cc_final: 0.8548 (tt0)
REVERT: a  284 LYS cc_start: 0.7005 (mttt) cc_final: 0.6456 (mmmt)
REVERT: b  349 MET cc_start: 0.7258 (mmt) cc_final: 0.7050 (mmm)
  outliers start: 39
  outliers final: 29
  residues processed: 157
  average time/residue: 1.2336
  time to fit residues: 208.9846
Evaluate side-chains
  163 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 128
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue   15 CYS
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   80 GLU
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain B residue   15 CYS
Chi-restraints excluded: chain B residue   30 ASP
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain a residue   13 THR
Chi-restraints excluded: chain a residue   89 VAL
Chi-restraints excluded: chain a residue  106 VAL
Chi-restraints excluded: chain a residue  220 MET
Chi-restraints excluded: chain a residue  224 GLU
Chi-restraints excluded: chain a residue  279 GLU
Chi-restraints excluded: chain b residue    2 VAL
Chi-restraints excluded: chain b residue   13 THR
Chi-restraints excluded: chain b residue   51 GLU
Chi-restraints excluded: chain b residue   97 MET
Chi-restraints excluded: chain b residue  162 VAL
Chi-restraints excluded: chain b residue  209 THR
Chi-restraints excluded: chain b residue  287 VAL
Chi-restraints excluded: chain b residue  351 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 84 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 132 optimal weight:    7.9990
   chunk 72 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 116 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 91 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
a 254 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.156229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.119715 restraints weight = 11688.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 2.21
r_work: 0.3209 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3061 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  11232  Z= 0.148
  Angle     :  0.712  25.949  15240  Z= 0.364
  Chirality :  0.044   0.257   1592
  Planarity :  0.004   0.063   1956
  Dihedral  :  4.589  21.960   1486
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 19.18 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.23), residues: 1352
  helix:  2.25 (0.42), residues: 154
  sheet: -1.63 (0.31), residues: 310
  loop : -0.88 (0.21), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP a  28 
 HIS   0.004   0.001   HIS a 254 
 PHE   0.010   0.001   PHE B 277 
 TYR   0.015   0.001   TYR A 122 
 ARG   0.013   0.000   ARG b 347 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03670 (  263)
  hydrogen bonds       : angle       5.42053 (  678)
  SS BOND              : bond        0.00596 (   24)
  SS BOND              : angle       3.79707 (   48)
  covalent geometry    : bond        0.00355 (11208)
  covalent geometry    : angle       0.68020 (15192)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8360.92 seconds
wall clock time: 144 minutes 27.44 seconds (8667.44 seconds total)