Starting phenix.real_space_refine
on Sat Aug 23 11:56:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c21_16387/08_2025/8c21_16387.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c21_16387/08_2025/8c21_16387.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c21_16387/08_2025/8c21_16387.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c21_16387/08_2025/8c21_16387.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c21_16387/08_2025/8c21_16387.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c21_16387/08_2025/8c21_16387.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.028
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      32      5.16       5
     C    7918      2.51       5
     N    1927      2.21       5
     O    2077      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11954
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 365, 3014
          Classifications: {'peptide': 365}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 344}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 3033
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 3033
          Classifications: {'peptide': 367}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 346}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3033
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 3033
          Classifications: {'peptide': 367}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 346}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 342, 2848
          Classifications: {'peptide': 342}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 324}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 13
          Unusual residues: {'SRO': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 13
          Unusual residues: {'SRO': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.07, per 1000 atoms: 0.26
  Number of scatterers: 11954
  At special positions: 0
  Unit cell: (89.559, 88.722, 130.572, 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      32     16.00
     O    2077      8.00
     N    1927      7.00
     C    7918      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 135 " - pdb=" SG  CYS A 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 135 " - pdb=" SG  CYS B 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 135 " - pdb=" SG  CYS C 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 135 " - pdb=" SG  CYS D 149 " 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: 1.03
  Conformation dependent library (CDL) restraints added in 458.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2806

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 17 sheets defined
      41.9% alpha, 23.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 22
      removed outlier: 4.741A  pdb=" N   ASN A  22 " --> pdb=" O   HIS A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 80
    Processing helix  chain 'A' and resid 170 through 176
      removed outlier: 3.798A  pdb=" N   SER A 176 " --> pdb=" O   GLU A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 225
      removed outlier: 4.445A  pdb=" N   VAL A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 244
    Processing helix  chain 'A' and resid 251 through 273
    Processing helix  chain 'A' and resid 281 through 311
      removed outlier: 4.015A  pdb=" N   VAL A 285 " --> pdb=" O   PRO A 281 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   TYR A 286 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLN A 311 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 328
    Processing helix  chain 'A' and resid 422 through 462
      removed outlier: 4.097A  pdb=" N   TRP A 426 " --> pdb=" O   VAL A 422 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL A 453 " --> pdb=" O   SER A 449 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   SER A 462 " --> pdb=" O   ILE A 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 21
    Processing helix  chain 'B' and resid 89 through 93
      removed outlier: 3.623A  pdb=" N   ILE B  93 " --> pdb=" O   THR B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 176
    Processing helix  chain 'B' and resid 220 through 227
    Processing helix  chain 'B' and resid 227 through 241
      removed outlier: 3.976A  pdb=" N   MET B 235 " --> pdb=" O   SER B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 244
      No H-bonds generated for 'chain 'B' and resid 242 through 244'
    Processing helix  chain 'B' and resid 249 through 273
      removed outlier: 3.616A  pdb=" N   SER B 253 " --> pdb=" O   GLY B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 309
      removed outlier: 3.847A  pdb=" N   VAL B 285 " --> pdb=" O   PRO B 281 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   TYR B 286 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU B 307 " --> pdb=" O   PHE B 303 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   VAL B 308 " --> pdb=" O   ILE B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 333
    Processing helix  chain 'B' and resid 423 through 462
    Processing helix  chain 'C' and resid 11 through 20
    Processing helix  chain 'C' and resid 89 through 93
      removed outlier: 3.560A  pdb=" N   ILE C  93 " --> pdb=" O   THR C  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 170 through 176
      removed outlier: 3.789A  pdb=" N   SER C 176 " --> pdb=" O   GLU C 172 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 220 through 244
      removed outlier: 4.409A  pdb=" N   LEU C 229 " --> pdb=" O   VAL C 225 " (cutoff:3.500A)
      Proline residue:  C 230  - end of helix
      removed outlier: 4.035A  pdb=" N   CYS C 243 " --> pdb=" O   ILE C 239 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 273
      removed outlier: 3.751A  pdb=" N   ILE C 256 " --> pdb=" O   VAL C 252 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   THR C 272 " --> pdb=" O   ILE C 268 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 281 through 305
    Processing helix  chain 'C' and resid 320 through 333
      removed outlier: 4.110A  pdb=" N   ASP C 327 " --> pdb=" O   HIS C 323 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ILE C 329 " --> pdb=" O   VAL C 325 " (cutoff:3.500A)
      removed outlier: 4.872A  pdb=" N   ALA C 330 " --> pdb=" O   LEU C 326 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 423 through 461
    Processing helix  chain 'D' and resid 14 through 22
      removed outlier: 4.071A  pdb=" N   ASN D  22 " --> pdb=" O   HIS D  18 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 178
      removed outlier: 4.334A  pdb=" N   VAL D 174 " --> pdb=" O   SER D 170 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   SER D 176 " --> pdb=" O   GLU D 172 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ASP D 177 " --> pdb=" O   GLU D 173 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   LYS D 178 " --> pdb=" O   VAL D 174 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 220 through 227
    Processing helix  chain 'D' and resid 227 through 242
      removed outlier: 3.529A  pdb=" N   PHE D 233 " --> pdb=" O   LEU D 229 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ASP D 238 " --> pdb=" O   LEU D 234 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ILE D 239 " --> pdb=" O   MET D 235 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 249 through 273
      removed outlier: 3.997A  pdb=" N   ILE D 267 " --> pdb=" O   SER D 263 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ILE D 268 " --> pdb=" O   VAL D 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 281 through 308
      removed outlier: 3.960A  pdb=" N   TYR D 286 " --> pdb=" O   LEU D 282 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL D 288 " --> pdb=" O   GLY D 284 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 319 through 330
      removed outlier: 3.698A  pdb=" N   HIS D 323 " --> pdb=" O   ASP D 319 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 423 through 462
      removed outlier: 3.790A  pdb=" N   ARG D 428 " --> pdb=" O   ARG D 424 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   VAL D 429 " --> pdb=" O   ASP D 425 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   SER D 462 " --> pdb=" O   ILE D 458 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 105
      removed outlier: 7.172A  pdb=" N   VAL A 132 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 105
      removed outlier: 7.172A  pdb=" N   VAL A 132 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   TYR A  61 " --> pdb=" O   ILE A  48 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   ILE A  48 " --> pdb=" O   TYR A  61 " (cutoff:3.500A)
      removed outlier: 8.521A  pdb=" N   TRP A  63 " --> pdb=" O   TYR A  46 " (cutoff:3.500A)
      removed outlier: 7.699A  pdb=" N   TYR A  46 " --> pdb=" O   TRP A  63 " (cutoff:3.500A)
      removed outlier: 7.961A  pdb=" N   ARG A  65 " --> pdb=" O   ILE A  44 " (cutoff:3.500A)
      removed outlier: 8.004A  pdb=" N   ILE A  44 " --> pdb=" O   ARG A  65 " (cutoff:3.500A)
      removed outlier: 8.260A  pdb=" N   TYR A  67 " --> pdb=" O   ASP A  42 " (cutoff:3.500A)
      removed outlier: 8.565A  pdb=" N   ASP A  42 " --> pdb=" O   TYR A  67 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 89
    Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 100
      removed outlier: 3.550A  pdb=" N   LEU A  99 " --> pdb=" O   THR A 154 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 99 through 100
      removed outlier: 3.550A  pdb=" N   LEU A  99 " --> pdb=" O   THR A 154 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   ASN A 205 " --> pdb=" O   SER A 200 " (cutoff:3.500A)
      removed outlier: 5.188A  pdb=" N   SER A 200 " --> pdb=" O   ASN A 205 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   TYR A 207 " --> pdb=" O   GLU A 198 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   GLU A 198 " --> pdb=" O   TYR A 207 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   GLU A 209 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 4.900A  pdb=" N   PHE A 196 " --> pdb=" O   GLU A 209 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   LYS A 211 " --> pdb=" O   PRO A 194 " (cutoff:3.500A)
      removed outlier: 5.943A  pdb=" N   TYR A 213 " --> pdb=" O   VAL A 192 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   VAL A 192 " --> pdb=" O   TYR A 213 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ILE A 215 " --> pdb=" O   LEU A 190 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 105
      removed outlier: 7.386A  pdb=" N   VAL B 132 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 103 through 105
      removed outlier: 7.386A  pdb=" N   VAL B 132 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   TYR B  61 " --> pdb=" O   ILE B  48 " (cutoff:3.500A)
      removed outlier: 5.565A  pdb=" N   ILE B  48 " --> pdb=" O   TYR B  61 " (cutoff:3.500A)
      removed outlier: 7.973A  pdb=" N   TRP B  63 " --> pdb=" O   TYR B  46 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   TYR B  46 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 7.756A  pdb=" N   ARG B  65 " --> pdb=" O   ILE B  44 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   ILE B  44 " --> pdb=" O   ARG B  65 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   TYR B  67 " --> pdb=" O   ASP B  42 " (cutoff:3.500A)
      removed outlier: 8.096A  pdb=" N   ASP B  42 " --> pdb=" O   TYR B  67 " (cutoff:3.500A)
      removed outlier: 8.613A  pdb=" N   THR B  69 " --> pdb=" O   SER B  40 " (cutoff:3.500A)
      removed outlier: 9.548A  pdb=" N   SER B  40 " --> pdb=" O   THR B  69 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 100
      removed outlier: 6.737A  pdb=" N   LYS B 211 " --> pdb=" O   PRO B 194 " (cutoff:3.500A)
      removed outlier: 5.706A  pdb=" N   TYR B 213 " --> pdb=" O   VAL B 192 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   VAL B 192 " --> pdb=" O   TYR B 213 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   ILE B 215 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 199 through 200
    Processing sheet with id=AB1, first strand: chain 'C' and resid 85 through 88
      removed outlier: 4.296A  pdb=" N   GLU C 122 " --> pdb=" O   HIS C 118 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   TRP C  68 " --> pdb=" O   VAL C 123 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   VAL C 132 " --> pdb=" O   ASP C 105 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 88
      removed outlier: 4.296A  pdb=" N   GLU C 122 " --> pdb=" O   HIS C 118 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   TRP C  68 " --> pdb=" O   VAL C 123 " (cutoff:3.500A)
      removed outlier: 5.700A  pdb=" N   TRP C  63 " --> pdb=" O   MET C  45 " (cutoff:3.500A)
      removed outlier: 5.572A  pdb=" N   MET C  45 " --> pdb=" O   TRP C  63 " (cutoff:3.500A)
      removed outlier: 7.596A  pdb=" N   ARG C  65 " --> pdb=" O   VAL C  43 " (cutoff:3.500A)
      removed outlier: 5.831A  pdb=" N   VAL C  43 " --> pdb=" O   ARG C  65 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   TYR C  67 " --> pdb=" O   ILE C  41 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   ILE C  41 " --> pdb=" O   TYR C  67 " (cutoff:3.500A)
      removed outlier: 8.669A  pdb=" N   THR C  69 " --> pdb=" O   VAL C  39 " (cutoff:3.500A)
      removed outlier: 8.356A  pdb=" N   VAL C  39 " --> pdb=" O   THR C  69 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 98 through 99
    Processing sheet with id=AB4, first strand: chain 'C' and resid 98 through 99
      removed outlier: 6.234A  pdb=" N   ARG C 217 " --> pdb=" O   LEU C 189 " (cutoff:3.500A)
      removed outlier: 5.128A  pdb=" N   LEU C 189 " --> pdb=" O   ARG C 217 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 40 through 41
      removed outlier: 3.740A  pdb=" N   GLN D  66 " --> pdb=" O   ASN D 125 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ASN D 125 " --> pdb=" O   GLN D  66 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ILE D  88 " --> pdb=" O   VAL D 115 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   VAL D 117 " --> pdb=" O   LEU D  86 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU D  86 " --> pdb=" O   VAL D 117 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 44 through 51
      removed outlier: 4.090A  pdb=" N   TYR D  61 " --> pdb=" O   TYR D  46 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ILE D  48 " --> pdb=" O   THR D  59 " (cutoff:3.500A)
      removed outlier: 8.548A  pdb=" N   THR D  59 " --> pdb=" O   ILE D  48 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 98 through 100
    Processing sheet with id=AB8, first strand: chain 'D' and resid 146 through 149
      removed outlier: 3.652A  pdb=" N   GLN D 147 " --> pdb=" O   ILE D 216 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   LYS D 211 " --> pdb=" O   PRO D 194 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   TYR D 213 " --> pdb=" O   VAL D 192 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   VAL D 192 " --> pdb=" O   TYR D 213 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   ILE D 215 " --> pdb=" O   LEU D 190 " (cutoff:3.500A)

    569 hydrogen bonds defined for protein.
    1650 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.72

  Time building geometry restraints manager: 1.39 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: 3623
        1.34 -     1.46: 2113
        1.46 -     1.57: 6511
        1.57 -     1.69: 0
        1.69 -     1.81: 48
  Bond restraints: 12295
  Sorted by residual:
  bond pdb=" CG  SRO C 501 "
       pdb=" CD2 SRO C 501 "
    ideal  model  delta    sigma   weight residual
    1.438  1.362  0.076 2.00e-02 2.50e+03 1.45e+01
  bond pdb=" CG  SRO B 501 "
       pdb=" CD2 SRO B 501 "
    ideal  model  delta    sigma   weight residual
    1.438  1.364  0.074 2.00e-02 2.50e+03 1.38e+01
  bond pdb=" N   ASP D 312 "
       pdb=" CA  ASP D 312 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.29e-02 6.01e+03 6.89e+00
  bond pdb=" CD2 SRO B 501 "
       pdb=" CE2 SRO B 501 "
    ideal  model  delta    sigma   weight residual
    1.419  1.368  0.051 2.00e-02 2.50e+03 6.61e+00
  bond pdb=" CD2 SRO C 501 "
       pdb=" CE2 SRO C 501 "
    ideal  model  delta    sigma   weight residual
    1.419  1.368  0.051 2.00e-02 2.50e+03 6.53e+00
  ... (remaining 12290 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 16550
        1.98 -     3.96: 230
        3.96 -     5.94: 30
        5.94 -     7.92: 6
        7.92 -     9.90: 3
  Bond angle restraints: 16819
  Sorted by residual:
  angle pdb=" N   VAL A 104 "
        pdb=" CA  VAL A 104 "
        pdb=" C   VAL A 104 "
      ideal   model   delta    sigma   weight residual
     111.62  108.53    3.09 7.90e-01 1.60e+00 1.53e+01
  angle pdb=" C   THR A 159 "
        pdb=" N   ILE A 160 "
        pdb=" CA  ILE A 160 "
      ideal   model   delta    sigma   weight residual
     121.97  128.66   -6.69 1.80e+00 3.09e-01 1.38e+01
  angle pdb=" CA  GLN A 161 "
        pdb=" CB  GLN A 161 "
        pdb=" CG  GLN A 161 "
      ideal   model   delta    sigma   weight residual
     114.10  121.21   -7.11 2.00e+00 2.50e-01 1.26e+01
  angle pdb=" N   LEU D 313 "
        pdb=" CA  LEU D 313 "
        pdb=" C   LEU D 313 "
      ideal   model   delta    sigma   weight residual
     112.58  108.27    4.31 1.22e+00 6.72e-01 1.25e+01
  angle pdb=" CB  SRO B 501 "
        pdb=" CG  SRO B 501 "
        pdb=" CD1 SRO B 501 "
      ideal   model   delta    sigma   weight residual
     128.15  118.25    9.90 3.00e+00 1.11e-01 1.09e+01
  ... (remaining 16814 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.46: 6444
       17.46 -    34.92: 596
       34.92 -    52.38: 125
       52.38 -    69.83: 18
       69.83 -    87.29: 17
  Dihedral angle restraints: 7200
    sinusoidal: 2898
      harmonic: 4302
  Sorted by residual:
  dihedral pdb=" CB  CYS B 135 "
           pdb=" SG  CYS B 135 "
           pdb=" SG  CYS B 149 "
           pdb=" CB  CYS B 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  141.13  -48.13     1      1.00e+01 1.00e-02 3.19e+01
  dihedral pdb=" CB  CYS A 135 "
           pdb=" SG  CYS A 135 "
           pdb=" SG  CYS A 149 "
           pdb=" CB  CYS A 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   49.15   43.85     1      1.00e+01 1.00e-02 2.68e+01
  dihedral pdb=" CB  CYS C 135 "
           pdb=" SG  CYS C 135 "
           pdb=" SG  CYS C 149 "
           pdb=" CB  CYS C 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   58.32   34.68     1      1.00e+01 1.00e-02 1.71e+01
  ... (remaining 7197 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1299
       0.036 -    0.073: 469
       0.073 -    0.109: 127
       0.109 -    0.145: 61
       0.145 -    0.182: 2
  Chirality restraints: 1958
  Sorted by residual:
  chirality pdb=" CB  ILE D 160 "
            pdb=" CA  ILE D 160 "
            pdb=" CG1 ILE D 160 "
            pdb=" CG2 ILE D 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.18 2.00e-01 2.50e+01 8.24e-01
  chirality pdb=" CA  VAL C 305 "
            pdb=" N   VAL C 305 "
            pdb=" C   VAL C 305 "
            pdb=" CB  VAL C 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.34e-01
  chirality pdb=" CA  VAL D 104 "
            pdb=" N   VAL D 104 "
            pdb=" C   VAL D 104 "
            pdb=" CB  VAL D 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.98e-01
  ... (remaining 1955 not shown)

  Planarity restraints: 2047
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 170 "   -0.036 5.00e-02 4.00e+02   5.52e-02 4.87e+00
        pdb=" N   PRO A 171 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 171 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 171 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 317 "    0.032 5.00e-02 4.00e+02   4.91e-02 3.86e+00
        pdb=" N   PRO C 318 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO C 318 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C 318 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 160 "   -0.009 2.00e-02 2.50e+03   1.85e-02 3.42e+00
        pdb=" C   ILE A 160 "    0.032 2.00e-02 2.50e+03
        pdb=" O   ILE A 160 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   GLN A 161 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 2044 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1740
        2.76 -     3.29: 11666
        3.29 -     3.83: 20126
        3.83 -     4.36: 22856
        4.36 -     4.90: 40360
  Nonbonded interactions: 96748
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 114 "
            pdb=" O   LYS D  25 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OG1 THR B 154 "
            pdb=" O   ALA B 208 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OE1 GLN C 124 "
            pdb=" OH  TYR C 126 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OD2 ASP D 434 "
            pdb=" NH2 ARG D 435 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" OE2 GLU B 122 "
            pdb=" NE2 GLN B 124 "
     model   vdw
     2.289 3.120
  ... (remaining 96743 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 13 through 75 or resid 85 through 105 or resid 113 through \ 
 181 or resid 186 through 332 or resid 422 through 462))
  selection = (chain 'B' and (resid 13 through 75 or resid 85 through 105 or resid 113 through \ 
 181 or resid 186 through 311 or resid 313 or resid 316 through 332 or resid 422 \ 
 through 462))
  selection = (chain 'C' and (resid 13 through 75 or resid 85 through 105 or resid 113 through \ 
 181 or resid 186 through 311 or resid 313 or resid 316 through 332 or resid 422 \ 
 through 462))
  selection = (chain 'D' and (resid 13 through 311 or resid 313 or resid 316 through 332 or re \ 
sid 422 through 462))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.540
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     11.590
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6784
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      :  0.003   0.076  12299  Z= 0.141
  Angle     :  0.576   9.900  16827  Z= 0.296
  Chirality :  0.043   0.182   1958
  Planarity :  0.004   0.055   2047
  Dihedral  : 14.613  87.293   4382
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  5.23 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.74 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.00 (0.23), residues: 1416
  helix:  2.06 (0.22), residues: 529
  sheet: -1.13 (0.30), residues: 312
  loop : -1.30 (0.27), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 120 
 TYR   0.019   0.001   TYR A 116 
 PHE   0.013   0.001   PHE B 254 
 TRP   0.018   0.001   TRP B 459 
 HIS   0.008   0.001   HIS D 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (12295)
  covalent geometry    : angle       0.57615 (16819)
  SS BOND              : bond        0.00082 (    4)
  SS BOND              : angle       0.55087 (    8)
  hydrogen bonds       : bond        0.16978 (  550)
  hydrogen bonds       : angle       6.62962 ( 1650)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  386 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 385
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  280 THR cc_start: 0.7451 (p) cc_final: 0.7194 (p)
REVERT: C  162 ASP cc_start: 0.5449 (m-30) cc_final: 0.5205 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 386
  average time/residue: 0.0958
  time to fit residues: 55.2337
Evaluate side-chains
  262 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:   30.0000
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    0.0070
   chunk 91 optimal weight:    9.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    2.0004

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
A 130 GLN
A 311 GLN
B  55 ASN
B 309 HIS
** D  66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 158 HIS
** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.099256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.076981 restraints weight = 40849.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.079498 restraints weight = 22032.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.081122 restraints weight = 14914.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.081949 restraints weight = 11669.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.082733 restraints weight = 10197.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.2320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079  12299  Z= 0.177
  Angle     :  0.650   9.198  16827  Z= 0.330
  Chirality :  0.045   0.154   1958
  Planarity :  0.005   0.049   2047
  Dihedral  :  5.715  67.598   1585
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 13.32
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  5.16 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 14.69 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.23), residues: 1416
  helix:  1.99 (0.22), residues: 548
  sheet: -1.07 (0.29), residues: 316
  loop : -1.30 (0.27), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 218 
 TYR   0.026   0.001   TYR C 114 
 PHE   0.014   0.002   PHE D 254 
 TRP   0.017   0.001   TRP B 156 
 HIS   0.007   0.001   HIS D 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (12295)
  covalent geometry    : angle       0.64703 (16819)
  SS BOND              : bond        0.00227 (    4)
  SS BOND              : angle       3.07392 (    8)
  hydrogen bonds       : bond        0.04144 (  550)
  hydrogen bonds       : angle       4.79028 ( 1650)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 284
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   59 THR cc_start: 0.9503 (m) cc_final: 0.9199 (p)
REVERT: B   97 ASP cc_start: 0.8010 (t70) cc_final: 0.7428 (t0)
REVERT: B  130 GLN cc_start: 0.8658 (tt0) cc_final: 0.8423 (tm-30)
REVERT: C   25 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8167 (ttmm)
REVERT: C  103 PHE cc_start: 0.8645 (t80) cc_final: 0.8205 (t80)
REVERT: C  125 ASN cc_start: 0.9001 (t0) cc_final: 0.8481 (t0)
REVERT: C  127 LYS cc_start: 0.9108 (ptmm) cc_final: 0.8578 (ptmm)
REVERT: C  130 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7951 (tm-30)
REVERT: C  235 MET cc_start: 0.9277 (mmm) cc_final: 0.9073 (mmm)
REVERT: C  441 TYR cc_start: 0.8412 (t80) cc_final: 0.8166 (t80)
REVERT: C  443 LEU cc_start: 0.9136 (mt) cc_final: 0.8794 (tt)
REVERT: D  156 TRP cc_start: 0.7271 (t-100) cc_final: 0.6717 (t-100)
REVERT: D  235 MET cc_start: 0.9129 (mmm) cc_final: 0.8689 (mmm)
REVERT: D  238 ASP cc_start: 0.8195 (t0) cc_final: 0.7988 (t0)
REVERT: D  441 TYR cc_start: 0.8696 (t80) cc_final: 0.8436 (t80)
REVERT: D  452 LEU cc_start: 0.9385 (mm) cc_final: 0.9180 (mm)
  outliers start: 34
  outliers final: 22
  residues processed: 298
  average time/residue: 0.0864
  time to fit residues: 39.7682
Evaluate side-chains
  267 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 245
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain B residue  257 THR
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  271 ASP
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  104 VAL
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain C residue  252 VAL
Chi-restraints excluded: chain C residue  256 ILE
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  442 LEU
Chi-restraints excluded: chain C residue  458 ILE
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue  131 LEU
Chi-restraints excluded: chain D residue  151 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 105 optimal weight:    9.9990
   chunk 70 optimal weight:    4.9990
   chunk 102 optimal weight:    0.6980
   chunk 46 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 131 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 14 optimal weight:   10.0000
   chunk 133 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
B 205 ASN
D 101 ASN
** D 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.097176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.075160 restraints weight = 41597.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.077535 restraints weight = 22549.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.079048 restraints weight = 15343.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.080027 restraints weight = 12048.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.080687 restraints weight = 10368.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  12299  Z= 0.213
  Angle     :  0.633   9.500  16827  Z= 0.322
  Chirality :  0.044   0.198   1958
  Planarity :  0.004   0.048   2047
  Dihedral  :  5.670  64.828   1585
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  4.80 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 16.99 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.23), residues: 1416
  helix:  2.11 (0.22), residues: 540
  sheet: -1.05 (0.29), residues: 311
  loop : -1.24 (0.27), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 219 
 TYR   0.024   0.001   TYR C  64 
 PHE   0.026   0.002   PHE C 254 
 TRP   0.018   0.001   TRP D  94 
 HIS   0.009   0.001   HIS C 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 (12295)
  covalent geometry    : angle       0.63222 (16819)
  SS BOND              : bond        0.00154 (    4)
  SS BOND              : angle       1.89269 (    8)
  hydrogen bonds       : bond        0.04025 (  550)
  hydrogen bonds       : angle       4.56037 ( 1650)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 264
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8824 (t0) cc_final: 0.8474 (t0)
REVERT: B   97 ASP cc_start: 0.8230 (t70) cc_final: 0.7648 (t0)
REVERT: B  130 GLN cc_start: 0.8682 (tt0) cc_final: 0.8460 (tm-30)
REVERT: C   25 LYS cc_start: 0.8504 (ttmm) cc_final: 0.8239 (ttmm)
REVERT: C   64 TYR cc_start: 0.8669 (t80) cc_final: 0.8297 (t80)
REVERT: C  103 PHE cc_start: 0.8676 (t80) cc_final: 0.8183 (t80)
REVERT: C  125 ASN cc_start: 0.9079 (t0) cc_final: 0.8461 (t0)
REVERT: C  127 LYS cc_start: 0.9111 (ptmm) cc_final: 0.8717 (ptmm)
REVERT: C  130 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7550 (tm-30)
REVERT: C  183 ASN cc_start: 0.9053 (t0) cc_final: 0.8724 (t0)
REVERT: C  443 LEU cc_start: 0.9159 (mt) cc_final: 0.8827 (tt)
REVERT: D   97 ASP cc_start: 0.7410 (p0) cc_final: 0.7202 (p0)
REVERT: D  156 TRP cc_start: 0.7340 (t-100) cc_final: 0.6898 (t-100)
  outliers start: 47
  outliers final: 31
  residues processed: 280
  average time/residue: 0.0846
  time to fit residues: 36.6063
Evaluate side-chains
  269 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 238
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 TYR
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  426 TRP
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain B residue   22 ASN
Chi-restraints excluded: chain B residue  257 THR
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  271 ASP
Chi-restraints excluded: chain B residue  290 CYS
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  443 LEU
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  104 VAL
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  256 ILE
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  442 LEU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain D residue  131 LEU
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  234 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 31 optimal weight:    8.9990
   chunk 35 optimal weight:    0.6980
   chunk 69 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 75 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 76 optimal weight:    4.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
B 205 ASN
C 314 GLN
** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.099397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.077506 restraints weight = 42333.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.079923 restraints weight = 23052.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.081490 restraints weight = 15735.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.082440 restraints weight = 12436.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.083099 restraints weight = 10723.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.3147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12299  Z= 0.163
  Angle     :  0.615  10.226  16827  Z= 0.309
  Chirality :  0.044   0.211   1958
  Planarity :  0.004   0.050   2047
  Dihedral  :  5.570  67.619   1585
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  4.94 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 18.62 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.23), residues: 1416
  helix:  2.20 (0.22), residues: 543
  sheet: -1.06 (0.29), residues: 312
  loop : -1.27 (0.27), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 175 
 TYR   0.020   0.001   TYR C  64 
 PHE   0.026   0.001   PHE D 254 
 TRP   0.016   0.001   TRP A 459 
 HIS   0.008   0.001   HIS C 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (12295)
  covalent geometry    : angle       0.61434 (16819)
  SS BOND              : bond        0.00742 (    4)
  SS BOND              : angle       1.00682 (    8)
  hydrogen bonds       : bond        0.03707 (  550)
  hydrogen bonds       : angle       4.43156 ( 1650)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 249
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8763 (t0) cc_final: 0.8224 (t0)
REVERT: A  167 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8057 (mp)
REVERT: B   97 ASP cc_start: 0.8109 (t70) cc_final: 0.7595 (t0)
REVERT: C   64 TYR cc_start: 0.8643 (t80) cc_final: 0.8341 (t80)
REVERT: C  103 PHE cc_start: 0.8573 (t80) cc_final: 0.8130 (t80)
REVERT: C  125 ASN cc_start: 0.9125 (t0) cc_final: 0.8571 (t0)
REVERT: C  130 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7058 (tm-30)
REVERT: C  183 ASN cc_start: 0.9013 (t0) cc_final: 0.8644 (t0)
REVERT: C  209 GLU cc_start: 0.8050 (tt0) cc_final: 0.7493 (tt0)
REVERT: C  443 LEU cc_start: 0.9193 (mt) cc_final: 0.8874 (tt)
REVERT: D  156 TRP cc_start: 0.7215 (t-100) cc_final: 0.6860 (t-100)
REVERT: D  441 TYR cc_start: 0.8472 (t80) cc_final: 0.8172 (t80)
  outliers start: 54
  outliers final: 35
  residues processed: 274
  average time/residue: 0.0804
  time to fit residues: 34.8805
Evaluate side-chains
  278 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 242
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 TYR
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  270 SER
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain B residue  257 THR
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  271 ASP
Chi-restraints excluded: chain B residue  290 CYS
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  443 LEU
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain C residue  253 SER
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  442 LEU
Chi-restraints excluded: chain C residue  458 ILE
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue  131 LEU
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  433 LEU
Chi-restraints excluded: chain D residue  434 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 81 optimal weight:    6.9990
   chunk 119 optimal weight:    0.2980
   chunk 78 optimal weight:    7.9990
   chunk 75 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 102 optimal weight:    0.8980
   chunk 137 optimal weight:    9.9990
   chunk 99 optimal weight:    6.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.098893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.077228 restraints weight = 41949.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.079633 restraints weight = 22779.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.081188 restraints weight = 15580.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.082023 restraints weight = 12240.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.082739 restraints weight = 10688.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.3354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12299  Z= 0.127
  Angle     :  0.605  11.250  16827  Z= 0.300
  Chirality :  0.044   0.222   1958
  Planarity :  0.004   0.050   2047
  Dihedral  :  5.606  79.137   1585
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  4.80 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 20.77 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.24), residues: 1416
  helix:  2.28 (0.22), residues: 544
  sheet: -0.98 (0.29), residues: 312
  loop : -1.18 (0.28), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 175 
 TYR   0.019   0.001   TYR C  64 
 PHE   0.027   0.001   PHE C 254 
 TRP   0.016   0.001   TRP A 459 
 HIS   0.007   0.001   HIS C 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (12295)
  covalent geometry    : angle       0.60480 (16819)
  SS BOND              : bond        0.00399 (    4)
  SS BOND              : angle       0.79680 (    8)
  hydrogen bonds       : bond        0.03508 (  550)
  hydrogen bonds       : angle       4.31098 ( 1650)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 256
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8796 (t0) cc_final: 0.8227 (t0)
REVERT: A  167 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8054 (mp)
REVERT: B   97 ASP cc_start: 0.8037 (t70) cc_final: 0.7555 (t0)
REVERT: C   64 TYR cc_start: 0.8616 (t80) cc_final: 0.8375 (t80)
REVERT: C  103 PHE cc_start: 0.8522 (t80) cc_final: 0.8075 (t80)
REVERT: C  125 ASN cc_start: 0.9090 (t0) cc_final: 0.8584 (t0)
REVERT: C  127 LYS cc_start: 0.9249 (ptmm) cc_final: 0.8815 (ptmm)
REVERT: C  130 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7719 (tm-30)
REVERT: C  183 ASN cc_start: 0.8990 (t0) cc_final: 0.8608 (t0)
REVERT: C  209 GLU cc_start: 0.7991 (tt0) cc_final: 0.7442 (tt0)
REVERT: C  443 LEU cc_start: 0.9207 (mt) cc_final: 0.8908 (tt)
REVERT: D   97 ASP cc_start: 0.7306 (p0) cc_final: 0.7095 (p0)
REVERT: D  156 TRP cc_start: 0.7265 (t-100) cc_final: 0.6859 (t-100)
REVERT: D  441 TYR cc_start: 0.8496 (t80) cc_final: 0.8238 (t80)
  outliers start: 41
  outliers final: 32
  residues processed: 275
  average time/residue: 0.0895
  time to fit residues: 38.0726
Evaluate side-chains
  270 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 237
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 TYR
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  426 TRP
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  271 ASP
Chi-restraints excluded: chain B residue  290 CYS
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain C residue  253 SER
Chi-restraints excluded: chain C residue  259 LEU
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  442 LEU
Chi-restraints excluded: chain C residue  458 ILE
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain D residue  131 LEU
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  433 LEU
Chi-restraints excluded: chain D residue  434 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 9 optimal weight:    0.1980
   chunk 24 optimal weight:    4.9990
   chunk 137 optimal weight:    7.9990
   chunk 8 optimal weight:    3.9990
   chunk 109 optimal weight:   10.0000
   chunk 127 optimal weight:    0.8980
   chunk 132 optimal weight:    0.4980
   chunk 119 optimal weight:    0.9980
   chunk 36 optimal weight:   10.0000
   chunk 105 optimal weight:    5.9990
   chunk 68 optimal weight:   20.0000
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
** C  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.098321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.076874 restraints weight = 41580.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.079296 restraints weight = 22363.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.080822 restraints weight = 15170.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.081854 restraints weight = 11855.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.082404 restraints weight = 10111.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.3532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12299  Z= 0.133
  Angle     :  0.610  11.297  16827  Z= 0.304
  Chirality :  0.045   0.201   1958
  Planarity :  0.004   0.046   2047
  Dihedral  :  5.522  76.303   1585
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  4.87 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 21.51 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.24), residues: 1416
  helix:  2.29 (0.22), residues: 541
  sheet: -0.96 (0.29), residues: 314
  loop : -1.18 (0.28), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 175 
 TYR   0.017   0.001   TYR C  64 
 PHE   0.019   0.001   PHE D 265 
 TRP   0.016   0.001   TRP B 331 
 HIS   0.009   0.001   HIS C 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (12295)
  covalent geometry    : angle       0.60857 (16819)
  SS BOND              : bond        0.00216 (    4)
  SS BOND              : angle       1.71614 (    8)
  hydrogen bonds       : bond        0.03508 (  550)
  hydrogen bonds       : angle       4.28898 ( 1650)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 251
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8839 (t0) cc_final: 0.8255 (t0)
REVERT: A  167 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8080 (mp)
REVERT: B   97 ASP cc_start: 0.8036 (t70) cc_final: 0.7584 (t0)
REVERT: B  262 TYR cc_start: 0.8738 (t80) cc_final: 0.8350 (t80)
REVERT: C  103 PHE cc_start: 0.8534 (t80) cc_final: 0.8071 (t80)
REVERT: C  125 ASN cc_start: 0.9098 (t0) cc_final: 0.8607 (t0)
REVERT: C  127 LYS cc_start: 0.9241 (ptmm) cc_final: 0.8580 (ptmm)
REVERT: C  130 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7724 (tm-30)
REVERT: C  162 ASP cc_start: 0.8759 (m-30) cc_final: 0.8360 (t0)
REVERT: C  183 ASN cc_start: 0.8978 (t0) cc_final: 0.8605 (t0)
REVERT: C  209 GLU cc_start: 0.7969 (tt0) cc_final: 0.7491 (tt0)
REVERT: C  254 PHE cc_start: 0.9288 (t80) cc_final: 0.8867 (t80)
REVERT: C  296 ILE cc_start: 0.9542 (mm) cc_final: 0.9329 (tp)
REVERT: C  443 LEU cc_start: 0.9198 (mt) cc_final: 0.8907 (tt)
REVERT: D   97 ASP cc_start: 0.7326 (p0) cc_final: 0.7116 (p0)
REVERT: D  156 TRP cc_start: 0.7334 (t-100) cc_final: 0.7053 (t-100)
REVERT: D  235 MET cc_start: 0.9056 (mmm) cc_final: 0.8839 (mmm)
REVERT: D  266 LEU cc_start: 0.9535 (tp) cc_final: 0.9333 (tp)
  outliers start: 48
  outliers final: 28
  residues processed: 275
  average time/residue: 0.0964
  time to fit residues: 41.0378
Evaluate side-chains
  261 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 232
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 TYR
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  271 ASP
Chi-restraints excluded: chain B residue  290 CYS
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain C residue  259 LEU
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain C residue  442 LEU
Chi-restraints excluded: chain C residue  458 ILE
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain D residue  131 LEU
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  433 LEU
Chi-restraints excluded: chain D residue  434 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 89 optimal weight:    9.9990
   chunk 19 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9990
   chunk 103 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 30 optimal weight:    9.9990
   chunk 134 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 126 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 323 HIS
B  66 GLN
** C  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.098539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.076589 restraints weight = 42401.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.078983 restraints weight = 22885.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.080525 restraints weight = 15601.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.081314 restraints weight = 12260.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.082044 restraints weight = 10779.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.3719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12299  Z= 0.200
  Angle     :  0.654  11.055  16827  Z= 0.326
  Chirality :  0.045   0.212   1958
  Planarity :  0.004   0.047   2047
  Dihedral  :  5.573  70.294   1585
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  5.37 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 23.22 %
    Favored  : 73.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.24), residues: 1416
  helix:  2.30 (0.22), residues: 541
  sheet: -1.04 (0.29), residues: 317
  loop : -1.15 (0.28), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 306 
 TYR   0.024   0.002   TYR D 441 
 PHE   0.020   0.001   PHE A 265 
 TRP   0.015   0.001   TRP B 331 
 HIS   0.006   0.001   HIS C 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 (12295)
  covalent geometry    : angle       0.65400 (16819)
  SS BOND              : bond        0.00294 (    4)
  SS BOND              : angle       0.95520 (    8)
  hydrogen bonds       : bond        0.03641 (  550)
  hydrogen bonds       : angle       4.39024 ( 1650)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 242
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8859 (t0) cc_final: 0.8265 (t0)
REVERT: A  167 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8113 (mp)
REVERT: B   97 ASP cc_start: 0.8063 (t70) cc_final: 0.7509 (t0)
REVERT: B  130 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8235 (tm-30)
REVERT: B  262 TYR cc_start: 0.8730 (t80) cc_final: 0.8409 (t80)
REVERT: C  103 PHE cc_start: 0.8668 (t80) cc_final: 0.8179 (t80)
REVERT: C  125 ASN cc_start: 0.9097 (t0) cc_final: 0.8613 (t0)
REVERT: C  127 LYS cc_start: 0.9256 (ptmm) cc_final: 0.8626 (ptmm)
REVERT: C  130 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7742 (tm-30)
REVERT: C  162 ASP cc_start: 0.8768 (m-30) cc_final: 0.8393 (t0)
REVERT: C  183 ASN cc_start: 0.9030 (t0) cc_final: 0.8679 (t0)
REVERT: C  254 PHE cc_start: 0.9347 (t80) cc_final: 0.8968 (t80)
REVERT: C  443 LEU cc_start: 0.9223 (mt) cc_final: 0.8939 (tt)
REVERT: D  156 TRP cc_start: 0.7411 (t-100) cc_final: 0.7070 (t-100)
  outliers start: 44
  outliers final: 32
  residues processed: 262
  average time/residue: 0.0761
  time to fit residues: 31.7025
Evaluate side-chains
  262 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 229
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 TYR
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  271 ASP
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain C residue  442 LEU
Chi-restraints excluded: chain C residue  458 ILE
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue  131 LEU
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  433 LEU
Chi-restraints excluded: chain D residue  434 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 138 optimal weight:    3.9990
   chunk 119 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   chunk 140 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** C  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.098416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.076971 restraints weight = 41839.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.079372 restraints weight = 22758.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.080923 restraints weight = 15614.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.081707 restraints weight = 12270.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.082363 restraints weight = 10787.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.3835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12299  Z= 0.119
  Angle     :  0.649  11.487  16827  Z= 0.316
  Chirality :  0.045   0.200   1958
  Planarity :  0.004   0.049   2047
  Dihedral  :  5.364  66.233   1585
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  4.80 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 24.41 %
    Favored  : 73.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.24), residues: 1416
  helix:  2.30 (0.22), residues: 540
  sheet: -0.92 (0.29), residues: 310
  loop : -1.12 (0.28), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 306 
 TYR   0.024   0.001   TYR C  64 
 PHE   0.019   0.001   PHE B 103 
 TRP   0.020   0.001   TRP B 331 
 HIS   0.008   0.001   HIS C 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (12295)
  covalent geometry    : angle       0.64858 (16819)
  SS BOND              : bond        0.00254 (    4)
  SS BOND              : angle       0.53281 (    8)
  hydrogen bonds       : bond        0.03440 (  550)
  hydrogen bonds       : angle       4.27334 ( 1650)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 251
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8829 (t0) cc_final: 0.8222 (t0)
REVERT: A  167 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8053 (mp)
REVERT: B   97 ASP cc_start: 0.7947 (t70) cc_final: 0.7439 (t0)
REVERT: B  262 TYR cc_start: 0.8677 (t80) cc_final: 0.8420 (t80)
REVERT: C  103 PHE cc_start: 0.8507 (t80) cc_final: 0.8062 (t80)
REVERT: C  125 ASN cc_start: 0.9084 (t0) cc_final: 0.8607 (t0)
REVERT: C  127 LYS cc_start: 0.9252 (ptmm) cc_final: 0.8605 (ptmm)
REVERT: C  130 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7821 (tm-30)
REVERT: C  162 ASP cc_start: 0.8749 (m-30) cc_final: 0.8363 (t0)
REVERT: C  183 ASN cc_start: 0.8991 (t0) cc_final: 0.8635 (t0)
REVERT: C  254 PHE cc_start: 0.9315 (t80) cc_final: 0.8917 (t80)
REVERT: C  443 LEU cc_start: 0.9210 (mt) cc_final: 0.8936 (tt)
REVERT: D   62 ILE cc_start: 0.9641 (OUTLIER) cc_final: 0.9351 (tp)
REVERT: D  156 TRP cc_start: 0.7431 (t-100) cc_final: 0.7090 (t-100)
REVERT: D  235 MET cc_start: 0.8856 (mmm) cc_final: 0.8414 (mmm)
REVERT: D  452 LEU cc_start: 0.9539 (mm) cc_final: 0.9336 (mm)
  outliers start: 35
  outliers final: 23
  residues processed: 272
  average time/residue: 0.0868
  time to fit residues: 36.8865
Evaluate side-chains
  257 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 232
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 TYR
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain C residue  442 LEU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain D residue  131 LEU
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  434 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 141 optimal weight:    0.7980
   chunk 54 optimal weight:    6.9990
   chunk 45 optimal weight:    0.5980
   chunk 136 optimal weight:    0.8980
   chunk 75 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 84 optimal weight:    0.1980
   chunk 124 optimal weight:    9.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  56 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.099185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.077492 restraints weight = 41868.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.079982 restraints weight = 22488.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.081559 restraints weight = 15262.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.082545 restraints weight = 11958.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.083049 restraints weight = 10264.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.3995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12299  Z= 0.118
  Angle     :  0.667  12.997  16827  Z= 0.320
  Chirality :  0.046   0.217   1958
  Planarity :  0.004   0.049   2047
  Dihedral  :  5.352  70.614   1585
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  4.94 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 25.00 %
    Favored  : 72.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.24), residues: 1416
  helix:  2.23 (0.22), residues: 540
  sheet: -0.84 (0.29), residues: 315
  loop : -1.16 (0.28), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 306 
 TYR   0.023   0.001   TYR C  64 
 PHE   0.034   0.001   PHE D 254 
 TRP   0.022   0.001   TRP B 331 
 HIS   0.013   0.001   HIS C 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (12295)
  covalent geometry    : angle       0.66708 (16819)
  SS BOND              : bond        0.00198 (    4)
  SS BOND              : angle       0.67137 (    8)
  hydrogen bonds       : bond        0.03471 (  550)
  hydrogen bonds       : angle       4.25254 ( 1650)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 235
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8855 (t0) cc_final: 0.8191 (t0)
REVERT: B   97 ASP cc_start: 0.7913 (t70) cc_final: 0.7422 (t0)
REVERT: B  130 GLN cc_start: 0.8396 (tm-30) cc_final: 0.7792 (pp30)
REVERT: B  262 TYR cc_start: 0.8632 (t80) cc_final: 0.8421 (t80)
REVERT: C   64 TYR cc_start: 0.8627 (t80) cc_final: 0.8399 (t80)
REVERT: C  103 PHE cc_start: 0.8299 (t80) cc_final: 0.7750 (t80)
REVERT: C  125 ASN cc_start: 0.9102 (t0) cc_final: 0.8602 (t0)
REVERT: C  127 LYS cc_start: 0.9251 (ptmm) cc_final: 0.8881 (ptmm)
REVERT: C  130 GLN cc_start: 0.8251 (tm-30) cc_final: 0.7696 (tm-30)
REVERT: C  162 ASP cc_start: 0.8791 (m-30) cc_final: 0.8408 (t0)
REVERT: C  183 ASN cc_start: 0.8990 (t0) cc_final: 0.8640 (t0)
REVERT: C  254 PHE cc_start: 0.9338 (t80) cc_final: 0.8954 (t80)
REVERT: C  443 LEU cc_start: 0.9194 (mt) cc_final: 0.8918 (tt)
REVERT: D   45 MET cc_start: 0.8690 (pmm) cc_final: 0.8071 (pmm)
REVERT: D  147 GLN cc_start: 0.8077 (mp10) cc_final: 0.7851 (mp10)
REVERT: D  156 TRP cc_start: 0.7464 (t-100) cc_final: 0.7166 (t-100)
REVERT: D  235 MET cc_start: 0.8804 (mmm) cc_final: 0.8531 (mmm)
  outliers start: 34
  outliers final: 23
  residues processed: 253
  average time/residue: 0.0835
  time to fit residues: 33.5043
Evaluate side-chains
  251 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 228
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 TYR
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain C residue  253 SER
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain C residue  442 LEU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue  131 LEU
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  434 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 79 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9990
   chunk 102 optimal weight:    9.9990
   chunk 120 optimal weight:    9.9990
   chunk 85 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9980
   chunk 136 optimal weight:    6.9990
   chunk 36 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.098747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.077147 restraints weight = 41739.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.079562 restraints weight = 22726.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.081069 restraints weight = 15541.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.081955 restraints weight = 12225.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.082609 restraints weight = 10596.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.4068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12299  Z= 0.141
  Angle     :  0.695  11.385  16827  Z= 0.340
  Chirality :  0.047   0.348   1958
  Planarity :  0.004   0.049   2047
  Dihedral  :  5.361  68.778   1585
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  4.80 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 25.89 %
    Favored  : 71.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.24), residues: 1416
  helix:  2.22 (0.22), residues: 540
  sheet: -0.85 (0.29), residues: 315
  loop : -1.15 (0.28), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 306 
 TYR   0.023   0.001   TYR C  64 
 PHE   0.033   0.001   PHE D 254 
 TRP   0.024   0.001   TRP B 331 
 HIS   0.012   0.001   HIS C 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (12295)
  covalent geometry    : angle       0.69452 (16819)
  SS BOND              : bond        0.00218 (    4)
  SS BOND              : angle       0.78370 (    8)
  hydrogen bonds       : bond        0.03581 (  550)
  hydrogen bonds       : angle       4.28360 ( 1650)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 233
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 LEU cc_start: 0.9182 (tp) cc_final: 0.8804 (tt)
REVERT: A  105 ASP cc_start: 0.8874 (t0) cc_final: 0.8246 (t0)
REVERT: B  130 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7854 (pp30)
REVERT: C  103 PHE cc_start: 0.8382 (t80) cc_final: 0.7866 (t80)
REVERT: C  125 ASN cc_start: 0.9109 (t0) cc_final: 0.8623 (t0)
REVERT: C  127 LYS cc_start: 0.9263 (ptmm) cc_final: 0.8663 (ptmm)
REVERT: C  130 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7736 (tm-30)
REVERT: C  162 ASP cc_start: 0.8791 (m-30) cc_final: 0.8416 (t0)
REVERT: C  183 ASN cc_start: 0.8999 (t0) cc_final: 0.8645 (t0)
REVERT: C  254 PHE cc_start: 0.9343 (t80) cc_final: 0.8965 (t80)
REVERT: C  443 LEU cc_start: 0.9193 (mt) cc_final: 0.8921 (tt)
REVERT: D   62 ILE cc_start: 0.9623 (OUTLIER) cc_final: 0.9331 (tp)
REVERT: D  156 TRP cc_start: 0.7581 (t-100) cc_final: 0.7266 (t-100)
REVERT: D  235 MET cc_start: 0.8816 (mmm) cc_final: 0.8280 (mmm)
  outliers start: 30
  outliers final: 25
  residues processed: 250
  average time/residue: 0.0768
  time to fit residues: 30.7954
Evaluate side-chains
  255 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 229
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 TYR
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  443 LEU
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain C residue  253 SER
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain C residue  442 LEU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain D residue  131 LEU
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  434 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 75 optimal weight:    8.9990
   chunk 103 optimal weight:    6.9990
   chunk 99 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 80 optimal weight:    0.0370
   chunk 47 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0970
   chunk 66 optimal weight:    0.4980
   chunk 8 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.7260

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

Flipped N/Q/H residues before XYZ refinement:
** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 309 HIS
D 323 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.099253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.078026 restraints weight = 41522.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.080392 restraints weight = 22550.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.081896 restraints weight = 15449.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.082729 restraints weight = 12202.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.083323 restraints weight = 10661.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.4213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  12299  Z= 0.123
  Angle     :  0.703  11.625  16827  Z= 0.339
  Chirality :  0.046   0.310   1958
  Planarity :  0.004   0.050   2047
  Dihedral  :  5.263  67.646   1585
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  4.87 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 26.48 %
    Favored  : 71.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.24), residues: 1416
  helix:  2.14 (0.22), residues: 540
  sheet: -0.79 (0.29), residues: 315
  loop : -1.17 (0.28), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  65 
 TYR   0.026   0.001   TYR C  64 
 PHE   0.031   0.001   PHE D 254 
 TRP   0.024   0.001   TRP B 331 
 HIS   0.014   0.001   HIS C 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (12295)
  covalent geometry    : angle       0.70281 (16819)
  SS BOND              : bond        0.00183 (    4)
  SS BOND              : angle       0.67341 (    8)
  hydrogen bonds       : bond        0.03500 (  550)
  hydrogen bonds       : angle       4.24274 ( 1650)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2086.09 seconds
wall clock time: 36 minutes 50.75 seconds (2210.75 seconds total)