Starting phenix.real_space_refine
on Mon May 19 06:24:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yei_39196/05_2025/8yei_39196.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yei_39196/05_2025/8yei_39196.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yei_39196/05_2025/8yei_39196.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yei_39196/05_2025/8yei_39196.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yei_39196/05_2025/8yei_39196.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yei_39196/05_2025/8yei_39196.cif"
  }
  resolution = 2.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.131
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     104      5.16       5
     C   11528      2.51       5
     N    3099      2.21       5
     O    3522      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 18253
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "H"
      Number of atoms: 946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 946
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 5, 'TRANS': 116}
    Chain: "L"
      Number of atoms: 837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 837
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 7, 'TRANS': 102}
    Chain: "A"
      Number of atoms: 3294
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 419, 3294
          Classifications: {'peptide': 419}
          Link IDs: {'PTRANS': 25, 'TRANS': 393}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3294
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 419, 3294
          Classifications: {'peptide': 419}
          Link IDs: {'PTRANS': 25, 'TRANS': 393}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 3294
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 419, 3294
          Classifications: {'peptide': 419}
          Link IDs: {'PTRANS': 25, 'TRANS': 393}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 3294
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 419, 3294
          Classifications: {'peptide': 419}
          Link IDs: {'PTRANS': 25, 'TRANS': 393}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3294
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 419, 3294
          Classifications: {'peptide': 419}
          Link IDs: {'PTRANS': 25, 'TRANS': 393}
          Chain breaks: 1
  Time building chain proxies: 10.10, per 1000 atoms: 0.55
  Number of scatterers: 18253
  At special positions: 0
  Unit cell: (115.44, 121.68, 134.16, 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     104     16.00
     O    3522      8.00
     N    3099      7.00
     C   11528      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  89 " 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: 4.59
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  4606 Ramachandran restraints generated.
    2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4306

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 24 sheets defined
      16.3% alpha, 18.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.87
  Creating SS restraints...
    Processing helix  chain 'H' and resid 61 through 64
    Processing helix  chain 'H' and resid 86 through 90
      removed outlier: 3.649A  pdb=" N   THR H  90 " --> pdb=" O   ALA H  87 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.720A  pdb=" N   GLU L  84 " --> pdb=" O   SER L  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 27
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 3.591A  pdb=" N   ILE A  90 " --> pdb=" O   ASP A  87 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   TYR A  91 " --> pdb=" O   THR A  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 87 through 91'
    Processing helix  chain 'A' and resid 209 through 214
    Processing helix  chain 'A' and resid 233 through 239
    Processing helix  chain 'A' and resid 272 through 276
    Processing helix  chain 'A' and resid 280 through 284
      removed outlier: 3.913A  pdb=" N   ARG A 283 " --> pdb=" O   THR A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 359
      No H-bonds generated for 'chain 'A' and resid 357 through 359'
    Processing helix  chain 'A' and resid 385 through 396
    Processing helix  chain 'A' and resid 397 through 404
    Processing helix  chain 'A' and resid 459 through 462
      removed outlier: 3.639A  pdb=" N   GLN A 462 " --> pdb=" O   ASP A 459 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 459 through 462'
    Processing helix  chain 'A' and resid 463 through 473
    Processing helix  chain 'B' and resid 23 through 26
    Processing helix  chain 'B' and resid 87 through 91
      removed outlier: 3.731A  pdb=" N   ILE B  90 " --> pdb=" O   ASP B  87 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   TYR B  91 " --> pdb=" O   THR B  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 87 through 91'
    Processing helix  chain 'B' and resid 209 through 214
    Processing helix  chain 'B' and resid 221 through 225
    Processing helix  chain 'B' and resid 233 through 239
    Processing helix  chain 'B' and resid 272 through 276
      removed outlier: 3.782A  pdb=" N   TYR B 276 " --> pdb=" O   GLN B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 284
      removed outlier: 3.743A  pdb=" N   ARG B 283 " --> pdb=" O   THR B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 303 through 305
      No H-bonds generated for 'chain 'B' and resid 303 through 305'
    Processing helix  chain 'B' and resid 357 through 359
      No H-bonds generated for 'chain 'B' and resid 357 through 359'
    Processing helix  chain 'B' and resid 385 through 396
    Processing helix  chain 'B' and resid 397 through 404
    Processing helix  chain 'B' and resid 459 through 462
    Processing helix  chain 'B' and resid 463 through 473
    Processing helix  chain 'D' and resid 23 through 27
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 3.583A  pdb=" N   ILE D  90 " --> pdb=" O   ASP D  87 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   TYR D  91 " --> pdb=" O   THR D  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 87 through 91'
    Processing helix  chain 'D' and resid 209 through 214
      removed outlier: 3.539A  pdb=" N   GLN D 214 " --> pdb=" O   PHE D 210 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 233 through 239
    Processing helix  chain 'D' and resid 272 through 276
      removed outlier: 3.701A  pdb=" N   TYR D 276 " --> pdb=" O   GLN D 273 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 280 through 284
    Processing helix  chain 'D' and resid 303 through 305
      No H-bonds generated for 'chain 'D' and resid 303 through 305'
    Processing helix  chain 'D' and resid 385 through 396
    Processing helix  chain 'D' and resid 396 through 404
      removed outlier: 4.384A  pdb=" N   LEU D 400 " --> pdb=" O   ASN D 396 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 459 through 462
      removed outlier: 3.590A  pdb=" N   GLN D 462 " --> pdb=" O   ASP D 459 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 459 through 462'
    Processing helix  chain 'D' and resid 463 through 473
    Processing helix  chain 'E' and resid 23 through 26
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.969A  pdb=" N   TYR E  91 " --> pdb=" O   THR E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 209 through 214
      removed outlier: 3.535A  pdb=" N   GLN E 214 " --> pdb=" O   PHE E 210 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 233 through 239
    Processing helix  chain 'E' and resid 272 through 276
    Processing helix  chain 'E' and resid 280 through 284
      removed outlier: 3.523A  pdb=" N   ARG E 283 " --> pdb=" O   THR E 280 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 303 through 305
      No H-bonds generated for 'chain 'E' and resid 303 through 305'
    Processing helix  chain 'E' and resid 357 through 359
      No H-bonds generated for 'chain 'E' and resid 357 through 359'
    Processing helix  chain 'E' and resid 385 through 396
    Processing helix  chain 'E' and resid 397 through 404
    Processing helix  chain 'E' and resid 463 through 473
    Processing helix  chain 'C' and resid 23 through 27
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.998A  pdb=" N   TYR C  91 " --> pdb=" O   THR C  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 214
      removed outlier: 3.638A  pdb=" N   GLN C 214 " --> pdb=" O   PHE C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 239
    Processing helix  chain 'C' and resid 272 through 276
      removed outlier: 3.560A  pdb=" N   TYR C 276 " --> pdb=" O   GLN C 273 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 280 through 284
    Processing helix  chain 'C' and resid 303 through 305
      No H-bonds generated for 'chain 'C' and resid 303 through 305'
    Processing helix  chain 'C' and resid 357 through 359
      No H-bonds generated for 'chain 'C' and resid 357 through 359'
    Processing helix  chain 'C' and resid 385 through 396
    Processing helix  chain 'C' and resid 396 through 404
      removed outlier: 4.418A  pdb=" N   LEU C 400 " --> pdb=" O   ASN C 396 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 459 through 462
      removed outlier: 3.572A  pdb=" N   GLN C 462 " --> pdb=" O   ASP C 459 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 459 through 462'
    Processing helix  chain 'C' and resid 463 through 473
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12
  WARNING: can't find start of bonding for strands!
    previous: chain 'H' and resid 11 through 12
    current: chain 'H' and resid 46 through 51
  WARNING: can't find start of bonding for strands!
    previous: chain 'H' and resid 57 through 59
    current: chain 'H' and resid 109 through 112
    Processing sheet with id=AA3, first strand: chain 'L' and resid 3 through 4
  WARNING: can't find start of bonding for strands!
    previous: chain 'L' and resid 3 through 4
    current: chain 'L' and resid 46 through 49
  WARNING: can't find start of bonding for strands!
    previous: chain 'L' and resid 46 through 49
    current: chain 'L' and resid 98 through 102
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'L' and resid 17 through 23
    Processing sheet with id=AA5, first strand: chain 'A' and resid 29 through 38
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 29 through 38
    current: chain 'A' and resid 310 through 312
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 310 through 312
    current: chain 'A' and resid 361 through 383
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 76
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 71 through 76
    current: chain 'A' and resid 248 through 261
      removed outlier: 6.197A  pdb=" N   SER A 294 " --> pdb=" O   ARG A 258 " (cutoff:3.500A)
      removed outlier: 4.852A  pdb=" N   PHE A 260 " --> pdb=" O   SER A 292 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   SER A 292 " --> pdb=" O   PHE A 260 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 118 through 123
      removed outlier: 4.134A  pdb=" N   PHE A 122 " --> pdb=" O   ASP A 145 " (cutoff:3.500A)
      removed outlier: 5.544A  pdb=" N   ASP A 145 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 188 through 194
      removed outlier: 5.343A  pdb=" N   TRP A 169 " --> pdb=" O   CYS A 229 " (cutoff:3.500A)
      removed outlier: 7.326A  pdb=" N   CYS A 229 " --> pdb=" O   TRP A 169 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   MET A 200 " --> pdb=" O   LYS A 230 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 266 through 267
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 266 through 267
    current: chain 'B' and resid 311 through 312
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 311 through 312
    current: chain 'B' and resid 361 through 383
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 300 through 301
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 300 through 301
    current: chain 'C' and resid 248 through 262
      removed outlier: 5.483A  pdb=" N   ALA C 257 " --> pdb=" O   SER C 296 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   SER C 296 " --> pdb=" O   ALA C 257 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   HIS C 259 " --> pdb=" O   SER C 294 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 71 through 76
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 71 through 76
    current: chain 'B' and resid 248 through 262
      removed outlier: 5.416A  pdb=" N   ALA B 257 " --> pdb=" O   SER B 296 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   SER B 296 " --> pdb=" O   ALA B 257 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   HIS B 259 " --> pdb=" O   SER B 294 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 118 through 123
      removed outlier: 4.289A  pdb=" N   PHE B 122 " --> pdb=" O   ASP B 145 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   ASP B 145 " --> pdb=" O   PHE B 122 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 188 through 194
      removed outlier: 5.436A  pdb=" N   TRP B 169 " --> pdb=" O   CYS B 229 " (cutoff:3.500A)
      removed outlier: 7.275A  pdb=" N   CYS B 229 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   MET B 200 " --> pdb=" O   LYS B 230 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 266 through 267
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 266 through 267
    current: chain 'D' and resid 311 through 312
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 311 through 312
    current: chain 'D' and resid 361 through 383
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'D' and resid 71 through 76
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 71 through 76
    current: chain 'D' and resid 248 through 262
      removed outlier: 6.176A  pdb=" N   SER D 294 " --> pdb=" O   ARG D 258 " (cutoff:3.500A)
      removed outlier: 4.845A  pdb=" N   PHE D 260 " --> pdb=" O   SER D 292 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   SER D 292 " --> pdb=" O   PHE D 260 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 118 through 123
      removed outlier: 4.984A  pdb=" N   GLY D 119 " --> pdb=" O   VAL D 149 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   VAL D 149 " --> pdb=" O   GLY D 119 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   VAL D 147 " --> pdb=" O   PRO D 121 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 188 through 194
      removed outlier: 5.421A  pdb=" N   TRP D 169 " --> pdb=" O   CYS D 229 " (cutoff:3.500A)
      removed outlier: 7.397A  pdb=" N   CYS D 229 " --> pdb=" O   TRP D 169 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   MET D 200 " --> pdb=" O   LYS D 230 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 266 through 267
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 266 through 267
    current: chain 'E' and resid 311 through 312
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 311 through 312
    current: chain 'E' and resid 361 through 383
  No H-bonds generated for sheet with id=AB9
    Processing sheet with id=AC1, first strand: chain 'E' and resid 71 through 76
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 71 through 76
    current: chain 'E' and resid 248 through 262
      removed outlier: 5.560A  pdb=" N   ALA E 257 " --> pdb=" O   SER E 296 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   SER E 296 " --> pdb=" O   ALA E 257 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   HIS E 259 " --> pdb=" O   SER E 294 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 118 through 123
      removed outlier: 4.281A  pdb=" N   PHE E 122 " --> pdb=" O   ASP E 145 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   ASP E 145 " --> pdb=" O   PHE E 122 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'E' and resid 188 through 194
      removed outlier: 5.452A  pdb=" N   TRP E 169 " --> pdb=" O   CYS E 229 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   CYS E 229 " --> pdb=" O   TRP E 169 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   MET E 200 " --> pdb=" O   LYS E 230 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'E' and resid 266 through 267
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 266 through 267
    current: chain 'C' and resid 310 through 312
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 310 through 312
    current: chain 'C' and resid 361 through 383
  No H-bonds generated for sheet with id=AC4
    Processing sheet with id=AC5, first strand: chain 'C' and resid 118 through 123
      removed outlier: 4.133A  pdb=" N   PHE C 122 " --> pdb=" O   ASP C 145 " (cutoff:3.500A)
      removed outlier: 5.492A  pdb=" N   ASP C 145 " --> pdb=" O   PHE C 122 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 188 through 194
      removed outlier: 5.340A  pdb=" N   TRP C 169 " --> pdb=" O   CYS C 229 " (cutoff:3.500A)
      removed outlier: 7.242A  pdb=" N   CYS C 229 " --> pdb=" O   TRP C 169 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   MET C 200 " --> pdb=" O   LYS C 230 " (cutoff:3.500A)

    252 hydrogen bonds defined for protein.
    642 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: 4.54

  Time building geometry restraints manager: 5.25 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: 5959
        1.34 -     1.46: 4367
        1.46 -     1.58: 8260
        1.58 -     1.70: 0
        1.70 -     1.81: 144
  Bond restraints: 18730
  Sorted by residual:
  bond pdb=" C   SER C 350 "
       pdb=" N   PRO C 351 "
    ideal  model  delta    sigma   weight residual
    1.334  1.357 -0.023 1.11e-02 8.12e+03 4.42e+00
  bond pdb=" C   SER A 350 "
       pdb=" N   PRO A 351 "
    ideal  model  delta    sigma   weight residual
    1.331  1.357 -0.026 1.28e-02 6.10e+03 3.99e+00
  bond pdb=" C   TYR E 463 "
       pdb=" N   PRO E 464 "
    ideal  model  delta    sigma   weight residual
    1.335  1.352 -0.017 1.30e-02 5.92e+03 1.75e+00
  bond pdb=" N   ASN C 404 "
       pdb=" CA  ASN C 404 "
    ideal  model  delta    sigma   weight residual
    1.458  1.482 -0.024 1.90e-02 2.77e+03 1.66e+00
  bond pdb=" N   ASN E 404 "
       pdb=" CA  ASN E 404 "
    ideal  model  delta    sigma   weight residual
    1.458  1.482 -0.024 1.90e-02 2.77e+03 1.59e+00
  ... (remaining 18725 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 24799
        1.83 -     3.65: 572
        3.65 -     5.48: 76
        5.48 -     7.31: 25
        7.31 -     9.14: 13
  Bond angle restraints: 25485
  Sorted by residual:
  angle pdb=" C   LEU E 400 "
        pdb=" N   GLU E 401 "
        pdb=" CA  GLU E 401 "
      ideal   model   delta    sigma   weight residual
     121.94  112.93    9.01 2.00e+00 2.50e-01 2.03e+01
  angle pdb=" C   ARG L  51 "
        pdb=" N   ASN L  52 "
        pdb=" CA  ASN L  52 "
      ideal   model   delta    sigma   weight residual
     121.54  129.78   -8.24 1.91e+00 2.74e-01 1.86e+01
  angle pdb=" C   SER C 140 "
        pdb=" N   GLU C 141 "
        pdb=" CA  GLU C 141 "
      ideal   model   delta    sigma   weight residual
     121.54  128.86   -7.32 1.91e+00 2.74e-01 1.47e+01
  angle pdb=" C   TRP C 403 "
        pdb=" N   ASN C 404 "
        pdb=" CA  ASN C 404 "
      ideal   model   delta    sigma   weight residual
     121.70  128.45   -6.75 1.80e+00 3.09e-01 1.41e+01
  angle pdb=" C   TRP E 403 "
        pdb=" N   ASN E 404 "
        pdb=" CA  ASN E 404 "
      ideal   model   delta    sigma   weight residual
     121.70  128.43   -6.73 1.80e+00 3.09e-01 1.40e+01
  ... (remaining 25480 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.36: 10137
       17.36 -    34.72: 793
       34.72 -    52.07: 102
       52.07 -    69.43: 29
       69.43 -    86.79: 22
  Dihedral angle restraints: 11083
    sinusoidal: 4346
      harmonic: 6737
  Sorted by residual:
  dihedral pdb=" CA  PRO A 221 "
           pdb=" C   PRO A 221 "
           pdb=" N   LEU A 222 "
           pdb=" CA  LEU A 222 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.71  -22.29     0      5.00e+00 4.00e-02 1.99e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  95 "
           pdb=" CB  CYS H  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   57.04   35.96     1      1.00e+01 1.00e-02 1.83e+01
  dihedral pdb=" CA  SER E 350 "
           pdb=" C   SER E 350 "
           pdb=" N   PRO E 351 "
           pdb=" CA  PRO E 351 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.72   21.28     0      5.00e+00 4.00e-02 1.81e+01
  ... (remaining 11080 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 2108
       0.052 -    0.105: 469
       0.105 -    0.157: 167
       0.157 -    0.210: 5
       0.210 -    0.262: 4
  Chirality restraints: 2753
  Sorted by residual:
  chirality pdb=" CB  VAL E 201 "
            pdb=" CA  VAL E 201 "
            pdb=" CG1 VAL E 201 "
            pdb=" CG2 VAL E 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.72e+00
  chirality pdb=" CB  VAL E 143 "
            pdb=" CA  VAL E 143 "
            pdb=" CG1 VAL E 143 "
            pdb=" CG2 VAL E 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.69e+00
  chirality pdb=" CB  VAL C 201 "
            pdb=" CA  VAL C 201 "
            pdb=" CG1 VAL C 201 "
            pdb=" CG2 VAL C 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.40e+00
  ... (remaining 2750 not shown)

  Planarity restraints: 3323
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN D  92 "   -0.076 5.00e-02 4.00e+02   1.15e-01 2.10e+01
        pdb=" N   PRO D  93 "    0.198 5.00e-02 4.00e+02
        pdb=" CA  PRO D  93 "   -0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO D  93 "   -0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C  92 "    0.073 5.00e-02 4.00e+02   1.11e-01 1.97e+01
        pdb=" N   PRO C  93 "   -0.192 5.00e-02 4.00e+02
        pdb=" CA  PRO C  93 "    0.059 5.00e-02 4.00e+02
        pdb=" CD  PRO C  93 "    0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN E  92 "    0.054 5.00e-02 4.00e+02   8.33e-02 1.11e+01
        pdb=" N   PRO E  93 "   -0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO E  93 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO E  93 "    0.046 5.00e-02 4.00e+02
  ... (remaining 3320 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 4911
        2.80 -     3.33: 15958
        3.33 -     3.85: 33652
        3.85 -     4.38: 40162
        4.38 -     4.90: 67914
  Nonbonded interactions: 162597
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 197 "
            pdb=" NZ  LYS A 446 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" O   ARG C 263 "
            pdb=" OG  SER C 288 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" NH2 ARG A 258 "
            pdb=" OE2 GLU C 130 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" OD1 ASN A 146 "
            pdb=" OH  TYR C 291 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" OH  TYR A 291 "
            pdb=" OD1 ASN B 146 "
     model   vdw
     2.295 3.040
  ... (remaining 162592 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'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.960
  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:          0.720
  Check model and map are aligned:         0.130
  Set scattering table:                    0.190
  Process input model:                     39.020
  Find NCS groups from input model:        0.550
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0038
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      :  0.004   0.043  18732  Z= 0.162
  Angle     :  0.698   9.137  25489  Z= 0.358
  Chirality :  0.050   0.262   2753
  Planarity :  0.006   0.115   3323
  Dihedral  : 13.128  86.788   6771
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.16), residues: 2303
  helix: -1.47 (0.31), residues: 186
  sheet: -0.27 (0.19), residues: 734
  loop : -0.81 (0.16), residues: 1383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 261 
 HIS   0.005   0.001   HIS E 367 
 PHE   0.027   0.002   PHE B 247 
 TYR   0.024   0.002   TYR B  91 
 ARG   0.011   0.001   ARG E 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19266 (  252)
  hydrogen bonds       : angle       6.98072 (  642)
  SS BOND              : bond        0.00080 (    2)
  SS BOND              : angle       0.70585 (    4)
  covalent geometry    : bond        0.00357 (18730)
  covalent geometry    : angle       0.69837 (25485)

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

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

  4606 Ramachandran restraints generated.
    2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4606 Ramachandran restraints generated.
    2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   22 VAL cc_start: 0.0956 (m) cc_final: 0.0646 (p)
REVERT: B  369 GLU cc_start: 0.2021 (mm-30) cc_final: -0.1921 (pt0)
REVERT: D   64 LYS cc_start: 0.1420 (tttt) cc_final: 0.0573 (pttt)
REVERT: D   97 ARG cc_start: 0.3573 (mmt-90) cc_final: 0.2603 (mpt90)
REVERT: E  128 ASP cc_start: 0.0787 (t70) cc_final: 0.0139 (t0)
REVERT: E  319 HIS cc_start: 0.0211 (m-70) cc_final: -0.0226 (m-70)
REVERT: E  350 SER cc_start: 0.4744 (p) cc_final: 0.4365 (m)
REVERT: E  389 MET cc_start: -0.1469 (ttp) cc_final: -0.2429 (mmm)
REVERT: E  399 ILE cc_start: 0.1104 (mt) cc_final: 0.0790 (mt)
REVERT: E  467 ARG cc_start: 0.3038 (mtt90) cc_final: 0.1501 (tpm170)
REVERT: C  267 MET cc_start: 0.0810 (mmt) cc_final: 0.0392 (mpt)
REVERT: C  335 ASP cc_start: 0.2494 (t0) cc_final: 0.1523 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.9668
  time to fit residues: 157.2416
Evaluate side-chains
  106 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 192 optimal weight:    3.9990
   chunk 172 optimal weight:    0.6980
   chunk 95 optimal weight:    0.1980
   chunk 59 optimal weight:    0.0980
   chunk 116 optimal weight:    6.9990
   chunk 92 optimal weight:    6.9990
   chunk 178 optimal weight:    0.9990
   chunk 69 optimal weight:    5.9990
   chunk 108 optimal weight:    4.9990
   chunk 133 optimal weight:    9.9990
   chunk 207 optimal weight:    0.9980
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 320 ASN
E 192 ASN
** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 254 GLN
** C 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5151 r_free = 0.5151 target = 0.309361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4969 r_free = 0.4969 target = 0.284272 restraints weight = 25120.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.4981 rms_B_bonded: 2.35
r_work: 0.4926 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work (final): 0.4926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0355
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  18732  Z= 0.110
  Angle     :  0.549   9.039  25489  Z= 0.278
  Chirality :  0.044   0.157   2753
  Planarity :  0.005   0.070   3323
  Dihedral  :  4.497  18.775   2527
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  4.82 %
    Favored  : 94.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.17), residues: 2303
  helix: -0.65 (0.34), residues: 185
  sheet: -0.24 (0.19), residues: 725
  loop : -0.74 (0.16), residues: 1393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 261 
 HIS   0.005   0.001   HIS C 367 
 PHE   0.018   0.002   PHE B  73 
 TYR   0.022   0.001   TYR D 364 
 ARG   0.007   0.001   ARG C 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03709 (  252)
  hydrogen bonds       : angle       5.51195 (  642)
  SS BOND              : bond        0.00088 (    2)
  SS BOND              : angle       0.60299 (    4)
  covalent geometry    : bond        0.00241 (18730)
  covalent geometry    : angle       0.54922 (25485)

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

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

  4606 Ramachandran restraints generated.
    2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4606 Ramachandran restraints generated.
    2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 1.843 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  377 PHE cc_start: 0.2602 (m-80) cc_final: 0.2326 (m-80)
REVERT: B  369 GLU cc_start: 0.2265 (mm-30) cc_final: 0.0969 (tp30)
REVERT: D   64 LYS cc_start: 0.2192 (tttt) cc_final: 0.1465 (pttt)
REVERT: D   97 ARG cc_start: 0.3921 (mmt-90) cc_final: 0.2126 (mmt180)
REVERT: D  366 ARG cc_start: 0.1820 (mmt-90) cc_final: -0.0310 (mmt180)
REVERT: E  246 MET cc_start: 0.1011 (OUTLIER) cc_final: 0.0533 (mmm)
REVERT: E  319 HIS cc_start: 0.0275 (m-70) cc_final: -0.0133 (m-70)
REVERT: E  350 SER cc_start: 0.5533 (p) cc_final: 0.5094 (m)
REVERT: E  389 MET cc_start: -0.0882 (ttp) cc_final: -0.2214 (mmt)
REVERT: E  399 ILE cc_start: 0.1802 (mt) cc_final: 0.1571 (mt)
REVERT: E  467 ARG cc_start: 0.2474 (mtt90) cc_final: 0.0735 (tpm170)
REVERT: C  280 THR cc_start: -0.0453 (m) cc_final: -0.0872 (p)
REVERT: C  282 MET cc_start: -0.0566 (pmm) cc_final: -0.1013 (ppp)
REVERT: C  389 MET cc_start: -0.2068 (mmm) cc_final: -0.2623 (mmm)
  outliers start: 18
  outliers final: 10
  residues processed: 117
  average time/residue: 1.0604
  time to fit residues: 144.7868
Evaluate side-chains
  112 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 2.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   94 HIS
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain B residue  200 MET
Chi-restraints excluded: chain B residue  208 MET
Chi-restraints excluded: chain B residue  246 MET
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain D residue  130 GLU
Chi-restraints excluded: chain E residue  202 ASP
Chi-restraints excluded: chain E residue  246 MET
Chi-restraints excluded: chain E residue  283 ARG
Chi-restraints excluded: chain C residue  246 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 181 optimal weight:    0.9980
   chunk 125 optimal weight:    0.0980
   chunk 184 optimal weight:    0.4980
   chunk 154 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 32 optimal weight:    9.9990
   chunk 155 optimal weight:    3.9990
   chunk 200 optimal weight:    0.9990
   chunk 217 optimal weight:    2.9990
   chunk 194 optimal weight:    1.9990
   chunk 205 optimal weight:    1.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
H  33 HIS
H  77 GLN
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 320 ASN
** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 308 ASN
D 168 HIS
** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 153 GLN
** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 259 HIS
** C 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5146 r_free = 0.5146 target = 0.308902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4973 r_free = 0.4973 target = 0.285856 restraints weight = 24932.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.4981 rms_B_bonded: 2.15
r_work: 0.4927 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work (final): 0.4927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0716
moved from start:          0.2550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  18732  Z= 0.126
  Angle     :  0.577   9.283  25489  Z= 0.293
  Chirality :  0.044   0.147   2753
  Planarity :  0.005   0.055   3323
  Dihedral  :  4.528  21.950   2527
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  8.41 %
    Favored  : 90.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.16), residues: 2303
  helix: -0.24 (0.35), residues: 186
  sheet: -0.62 (0.18), residues: 767
  loop : -0.79 (0.16), residues: 1350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  34 
 HIS   0.008   0.001   HIS C 367 
 PHE   0.020   0.002   PHE B  73 
 TYR   0.021   0.002   TYR C 364 
 ARG   0.006   0.001   ARG B 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03407 (  252)
  hydrogen bonds       : angle       5.39360 (  642)
  SS BOND              : bond        0.00263 (    2)
  SS BOND              : angle       0.79482 (    4)
  covalent geometry    : bond        0.00281 (18730)
  covalent geometry    : angle       0.57746 (25485)

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

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

  4606 Ramachandran restraints generated.
    2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4606 Ramachandran restraints generated.
    2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 1.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  242 TYR cc_start: 0.2170 (m-80) cc_final: 0.0202 (m-80)
REVERT: B  369 GLU cc_start: 0.2310 (mm-30) cc_final: 0.0839 (tp30)
REVERT: D   64 LYS cc_start: 0.1896 (tttt) cc_final: 0.1529 (pttt)
REVERT: D   97 ARG cc_start: 0.4310 (mmt-90) cc_final: 0.2559 (mmt180)
REVERT: D  356 TYR cc_start: 0.3973 (t80) cc_final: 0.2732 (t80)
REVERT: E   44 THR cc_start: 0.0318 (p) cc_final: -0.0796 (t)
REVERT: E  200 MET cc_start: 0.3824 (ptp) cc_final: 0.2562 (mpt)
REVERT: E  246 MET cc_start: 0.1098 (OUTLIER) cc_final: 0.0889 (mmm)
REVERT: E  282 MET cc_start: 0.1683 (tmt) cc_final: 0.0451 (mmp)
REVERT: E  283 ARG cc_start: 0.3135 (OUTLIER) cc_final: 0.1920 (tpp-160)
REVERT: E  319 HIS cc_start: 0.0618 (m-70) cc_final: 0.0173 (m-70)
REVERT: E  350 SER cc_start: 0.5450 (p) cc_final: 0.4965 (m)
REVERT: E  389 MET cc_start: -0.0239 (ttp) cc_final: -0.1808 (mmt)
REVERT: E  399 ILE cc_start: 0.1768 (mt) cc_final: 0.1504 (mt)
REVERT: E  450 VAL cc_start: 0.4975 (m) cc_final: 0.4552 (t)
REVERT: E  467 ARG cc_start: 0.2748 (mtt90) cc_final: 0.0602 (tpp80)
REVERT: C  389 MET cc_start: -0.2085 (mmm) cc_final: -0.2505 (tmm)
  outliers start: 22
  outliers final: 14
  residues processed: 114
  average time/residue: 0.9742
  time to fit residues: 130.6914
Evaluate side-chains
  114 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 1.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain B residue  200 MET
Chi-restraints excluded: chain B residue  246 MET
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain D residue  130 GLU
Chi-restraints excluded: chain D residue  245 SER
Chi-restraints excluded: chain E residue  202 ASP
Chi-restraints excluded: chain E residue  246 MET
Chi-restraints excluded: chain E residue  283 ARG
Chi-restraints excluded: chain E residue  333 VAL
Chi-restraints excluded: chain C residue  120 HIS
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  267 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 73 optimal weight:    0.8980
   chunk 224 optimal weight:   20.0000
   chunk 135 optimal weight:    9.9990
   chunk 83 optimal weight:    3.9990
   chunk 98 optimal weight:    4.9990
   chunk 113 optimal weight:    7.9990
   chunk 16 optimal weight:    4.9990
   chunk 145 optimal weight:    4.9990
   chunk 170 optimal weight:    6.9990
   chunk 80 optimal weight:    0.0040
   overall best weight:    2.9798

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

Flipped N/Q/H residues before XYZ refinement:
A 155 GLN
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 327 ASN
** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 124 ASN
** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 314 HIS
D  47 ASN
** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 155 GLN
** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 327 ASN
** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 111 GLN
** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 168 HIS
E 259 HIS
E 321 ASN
** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 273 GLN
C 308 ASN
** C 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 462 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5162 r_free = 0.5162 target = 0.310965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.5027 r_free = 0.5027 target = 0.293542 restraints weight = 25259.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.5036 rms_B_bonded: 1.93
r_work: 0.4986 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.4886 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.4886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1744
moved from start:          0.5650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.084  18732  Z= 0.304
  Angle     :  1.014  16.427  25489  Z= 0.529
  Chirality :  0.057   0.316   2753
  Planarity :  0.008   0.078   3323
  Dihedral  :  7.046  31.611   2527
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 27.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 11.17 %
    Favored  : 85.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.16), residues: 2303
  helix: -1.12 (0.34), residues: 187
  sheet: -1.52 (0.19), residues: 657
  loop : -1.36 (0.15), residues: 1459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.003   TRP B 169 
 HIS   0.019   0.004   HIS B 120 
 PHE   0.041   0.004   PHE B 361 
 TYR   0.055   0.004   TYR A  49 
 ARG   0.012   0.002   ARG E  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04815 (  252)
  hydrogen bonds       : angle       7.93113 (  642)
  SS BOND              : bond        0.01127 (    2)
  SS BOND              : angle       2.53398 (    4)
  covalent geometry    : bond        0.00680 (18730)
  covalent geometry    : angle       1.01328 (25485)

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

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

  4606 Ramachandran restraints generated.
    2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4606 Ramachandran restraints generated.
    2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 109
  time to evaluate  : 2.070 
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: A  267 MET cc_start: 0.3798 (pmm) cc_final: 0.1874 (mpp)
REVERT: A  282 MET cc_start: 0.0920 (OUTLIER) cc_final: -0.3048 (mmt)
REVERT: A  377 PHE cc_start: 0.3058 (m-80) cc_final: 0.2529 (m-80)
REVERT: B   50 PHE cc_start: 0.2135 (OUTLIER) cc_final: 0.1801 (p90)
REVERT: B  283 ARG cc_start: 0.0349 (OUTLIER) cc_final: -0.0270 (ptp90)
REVERT: B  369 GLU cc_start: 0.3936 (mm-30) cc_final: 0.3083 (tp30)
REVERT: D   64 LYS cc_start: 0.3565 (tttt) cc_final: 0.2559 (ptpt)
REVERT: D   97 ARG cc_start: 0.4781 (mmt-90) cc_final: 0.4553 (mmp-170)
REVERT: D  130 GLU cc_start: 0.3757 (OUTLIER) cc_final: 0.3163 (pp20)
REVERT: E   41 ARG cc_start: 0.2686 (ttm-80) cc_final: 0.1734 (mtp-110)
REVERT: E   50 PHE cc_start: 0.0429 (OUTLIER) cc_final: -0.0098 (p90)
REVERT: E  200 MET cc_start: 0.4529 (ptp) cc_final: 0.3270 (mpp)
REVERT: E  246 MET cc_start: 0.3343 (OUTLIER) cc_final: 0.0687 (mmt)
REVERT: E  247 PHE cc_start: 0.3155 (OUTLIER) cc_final: 0.2078 (p90)
REVERT: E  282 MET cc_start: 0.2798 (tmt) cc_final: 0.0730 (mmp)
REVERT: E  283 ARG cc_start: 0.3854 (OUTLIER) cc_final: 0.2436 (tpp-160)
REVERT: E  319 HIS cc_start: 0.1509 (m-70) cc_final: 0.0766 (m-70)
REVERT: E  467 ARG cc_start: 0.3359 (mtt90) cc_final: 0.0078 (tpt-90)
REVERT: C  255 LEU cc_start: 0.4130 (OUTLIER) cc_final: 0.3492 (pp)
REVERT: C  306 LEU cc_start: 0.2112 (OUTLIER) cc_final: 0.1767 (mt)
REVERT: C  308 ASN cc_start: 0.0454 (OUTLIER) cc_final: -0.1864 (m110)
REVERT: C  389 MET cc_start: -0.2216 (mmm) cc_final: -0.2630 (tmm)
  outliers start: 70
  outliers final: 26
  residues processed: 159
  average time/residue: 0.9832
  time to fit residues: 183.2963
Evaluate side-chains
  137 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 100
  time to evaluate  : 1.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  294 SER
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain B residue   50 PHE
Chi-restraints excluded: chain B residue  200 MET
Chi-restraints excluded: chain B residue  208 MET
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  283 ARG
Chi-restraints excluded: chain B residue  375 PHE
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  130 GLU
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  333 VAL
Chi-restraints excluded: chain D residue  450 VAL
Chi-restraints excluded: chain E residue   24 THR
Chi-restraints excluded: chain E residue   50 PHE
Chi-restraints excluded: chain E residue   73 PHE
Chi-restraints excluded: chain E residue  125 LYS
Chi-restraints excluded: chain E residue  202 ASP
Chi-restraints excluded: chain E residue  242 TYR
Chi-restraints excluded: chain E residue  246 MET
Chi-restraints excluded: chain E residue  247 PHE
Chi-restraints excluded: chain E residue  283 ARG
Chi-restraints excluded: chain E residue  333 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  308 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 13 optimal weight:   20.0000
   chunk 140 optimal weight:    4.9990
   chunk 170 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 159 optimal weight:    0.9980
   chunk 96 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 106 optimal weight:    7.9990
   chunk 93 optimal weight:    0.9980
   chunk 171 optimal weight:    3.9990
   chunk 8 optimal weight:    7.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** L  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 133 HIS
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  92 ASN
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 124 ASN
** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 124 ASN
D 155 GLN
** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 111 GLN
E 155 GLN
** E 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 396 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5160 r_free = 0.5160 target = 0.310199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.5022 r_free = 0.5022 target = 0.291923 restraints weight = 25312.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.5035 rms_B_bonded: 1.95
r_work: 0.4983 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.4883 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.4883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1577
moved from start:          0.5726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075  18732  Z= 0.156
  Angle     :  0.651   7.861  25489  Z= 0.337
  Chirality :  0.047   0.202   2753
  Planarity :  0.005   0.061   3323
  Dihedral  :  5.736  24.686   2527
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 18.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 13.13 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.99 (0.16), residues: 2303
  helix: -1.31 (0.32), residues: 213
  sheet: -1.15 (0.20), residues: 558
  loop : -1.43 (0.15), residues: 1532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 448 
 HIS   0.007   0.002   HIS C 367 
 PHE   0.019   0.002   PHE E  73 
 TYR   0.025   0.002   TYR D 442 
 ARG   0.012   0.001   ARG B  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03564 (  252)
  hydrogen bonds       : angle       6.62315 (  642)
  SS BOND              : bond        0.00438 (    2)
  SS BOND              : angle       0.94388 (    4)
  covalent geometry    : bond        0.00354 (18730)
  covalent geometry    : angle       0.65110 (25485)

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

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

  4606 Ramachandran restraints generated.
    2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4606 Ramachandran restraints generated.
    2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 106
  time to evaluate  : 2.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 MET cc_start: 0.3496 (pmm) cc_final: 0.2624 (ptp)
REVERT: A  282 MET cc_start: 0.1084 (tmt) cc_final: -0.2800 (mmm)
REVERT: A  371 TYR cc_start: 0.3502 (m-80) cc_final: 0.2184 (m-80)
REVERT: A  377 PHE cc_start: 0.3060 (m-80) cc_final: 0.2187 (m-80)
REVERT: B  255 LEU cc_start: 0.2516 (OUTLIER) cc_final: 0.2218 (pp)
REVERT: B  330 PHE cc_start: 0.3348 (m-80) cc_final: 0.2917 (m-80)
REVERT: D  130 GLU cc_start: 0.3478 (OUTLIER) cc_final: 0.3271 (pt0)
REVERT: E   41 ARG cc_start: 0.2317 (ttm-80) cc_final: 0.1582 (mtp180)
REVERT: E  153 GLN cc_start: 0.2942 (OUTLIER) cc_final: 0.2724 (mt0)
REVERT: E  184 ASP cc_start: 0.1287 (m-30) cc_final: 0.0783 (t0)
REVERT: E  200 MET cc_start: 0.4194 (ptp) cc_final: 0.3733 (mpp)
REVERT: E  282 MET cc_start: 0.2414 (tmt) cc_final: 0.0241 (mmp)
REVERT: E  283 ARG cc_start: 0.3796 (OUTLIER) cc_final: 0.1962 (tpp-160)
REVERT: E  319 HIS cc_start: 0.1805 (m-70) cc_final: 0.1138 (m-70)
REVERT: E  467 ARG cc_start: 0.3424 (mtt90) cc_final: 0.0480 (tpp80)
REVERT: C  255 LEU cc_start: 0.3641 (OUTLIER) cc_final: 0.3292 (pp)
REVERT: C  389 MET cc_start: -0.2226 (mmm) cc_final: -0.2814 (tmm)
  outliers start: 59
  outliers final: 30
  residues processed: 149
  average time/residue: 0.9762
  time to fit residues: 172.5649
Evaluate side-chains
  134 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 99
  time to evaluate  : 1.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue  133 HIS
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain B residue  200 MET
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  327 ASN
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain B residue  375 PHE
Chi-restraints excluded: chain D residue  129 THR
Chi-restraints excluded: chain D residue  130 GLU
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  267 MET
Chi-restraints excluded: chain D residue  333 VAL
Chi-restraints excluded: chain D residue  452 LEU
Chi-restraints excluded: chain E residue   45 VAL
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  153 GLN
Chi-restraints excluded: chain E residue  202 ASP
Chi-restraints excluded: chain E residue  242 TYR
Chi-restraints excluded: chain E residue  256 PHE
Chi-restraints excluded: chain E residue  283 ARG
Chi-restraints excluded: chain E residue  333 VAL
Chi-restraints excluded: chain E residue  375 PHE
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  120 HIS
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  267 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 114 optimal weight:    9.9990
   chunk 218 optimal weight:    4.9990
   chunk 93 optimal weight:    1.9990
   chunk 227 optimal weight:    0.9980
   chunk 129 optimal weight:    0.4980
   chunk 46 optimal weight:    5.9990
   chunk 163 optimal weight:   10.0000
   chunk 79 optimal weight:    5.9990
   chunk 209 optimal weight:    0.0870
   chunk 196 optimal weight:    0.9990
   overall best weight:    0.9162

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

Flipped N/Q/H residues before XYZ refinement:
H  94 HIS
** L  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  92 ASN
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 GLN
** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 ASN
D 155 GLN
** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 317 GLN
** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 273 GLN
C 308 ASN
** C 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5157 r_free = 0.5157 target = 0.310172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.5019 r_free = 0.5019 target = 0.291760 restraints weight = 25306.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.5026 rms_B_bonded: 1.96
r_work: 0.4978 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.4878 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.4878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1545
moved from start:          0.5945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  18732  Z= 0.125
  Angle     :  0.603   9.343  25489  Z= 0.309
  Chirality :  0.045   0.241   2753
  Planarity :  0.005   0.051   3323
  Dihedral  :  5.293  25.471   2527
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.07 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.85 (0.16), residues: 2303
  helix: -0.83 (0.34), residues: 206
  sheet: -1.32 (0.20), residues: 630
  loop : -1.25 (0.15), residues: 1467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E 261 
 HIS   0.015   0.001   HIS A 133 
 PHE   0.014   0.002   PHE C 256 
 TYR   0.021   0.002   TYR B 371 
 ARG   0.008   0.001   ARG B 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03345 (  252)
  hydrogen bonds       : angle       6.08465 (  642)
  SS BOND              : bond        0.00384 (    2)
  SS BOND              : angle       0.77947 (    4)
  covalent geometry    : bond        0.00282 (18730)
  covalent geometry    : angle       0.60306 (25485)

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

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

  4606 Ramachandran restraints generated.
    2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4606 Ramachandran restraints generated.
    2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 95
  time to evaluate  : 1.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 MET cc_start: 0.3430 (pmm) cc_final: 0.2426 (ptp)
REVERT: A  282 MET cc_start: 0.0739 (tmt) cc_final: -0.2897 (mmt)
REVERT: A  371 TYR cc_start: 0.3301 (m-80) cc_final: 0.2127 (m-80)
REVERT: B  255 LEU cc_start: 0.2467 (OUTLIER) cc_final: 0.2174 (pp)
REVERT: B  330 PHE cc_start: 0.3274 (m-80) cc_final: 0.2669 (m-80)
REVERT: B  369 GLU cc_start: 0.2198 (tp30) cc_final: 0.1934 (tp30)
REVERT: B  389 MET cc_start: 0.0698 (ttt) cc_final: -0.0524 (pp-130)
REVERT: E   99 VAL cc_start: -0.2595 (OUTLIER) cc_final: -0.2860 (t)
REVERT: E  200 MET cc_start: 0.4132 (ptp) cc_final: 0.3852 (mpp)
REVERT: E  237 MET cc_start: 0.1628 (mmm) cc_final: 0.0536 (mmm)
REVERT: E  282 MET cc_start: 0.2463 (tmt) cc_final: 0.0462 (mmp)
REVERT: E  319 HIS cc_start: 0.1597 (m-70) cc_final: 0.1076 (m-70)
REVERT: E  467 ARG cc_start: 0.3210 (mtt90) cc_final: 0.0408 (tpp80)
REVERT: C  255 LEU cc_start: 0.3564 (OUTLIER) cc_final: 0.3131 (pp)
REVERT: C  389 MET cc_start: -0.2116 (mmm) cc_final: -0.2694 (mmm)
  outliers start: 53
  outliers final: 33
  residues processed: 135
  average time/residue: 0.9252
  time to fit residues: 147.4905
Evaluate side-chains
  125 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 89
  time to evaluate  : 1.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 ASN
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   73 PHE
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain B residue  200 MET
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  327 ASN
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain B residue  375 PHE
Chi-restraints excluded: chain D residue  201 VAL
Chi-restraints excluded: chain D residue  452 LEU
Chi-restraints excluded: chain E residue   73 PHE
Chi-restraints excluded: chain E residue   99 VAL
Chi-restraints excluded: chain E residue  125 LYS
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  202 ASP
Chi-restraints excluded: chain E residue  242 TYR
Chi-restraints excluded: chain E residue  247 PHE
Chi-restraints excluded: chain E residue  256 PHE
Chi-restraints excluded: chain E residue  333 VAL
Chi-restraints excluded: chain E residue  350 SER
Chi-restraints excluded: chain E residue  375 PHE
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  120 HIS
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  267 MET
Chi-restraints excluded: chain C residue  450 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 223 optimal weight:    0.9980
   chunk 135 optimal weight:    6.9990
   chunk 220 optimal weight:    1.9990
   chunk 175 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 167 optimal weight:    1.9990
   chunk 166 optimal weight:    0.0770
   chunk 94 optimal weight:    4.9990
   chunk 54 optimal weight:    6.9990
   chunk 140 optimal weight:    0.7980
   chunk 185 optimal weight:    0.9990
   overall best weight:    0.9742

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

Flipped N/Q/H residues before XYZ refinement:
H  94 HIS
** L  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  92 ASN
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 155 GLN
** C 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5157 r_free = 0.5157 target = 0.310102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.5022 r_free = 0.5022 target = 0.292029 restraints weight = 25187.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.5030 rms_B_bonded: 1.92
r_work: 0.4981 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.4881 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.4881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1596
moved from start:          0.6343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  18732  Z= 0.124
  Angle     :  0.595   9.124  25489  Z= 0.303
  Chirality :  0.045   0.215   2753
  Planarity :  0.004   0.047   3323
  Dihedral  :  5.101  23.977   2527
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 14.51 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.16), residues: 2303
  helix: -0.59 (0.35), residues: 199
  sheet: -1.21 (0.21), residues: 601
  loop : -1.22 (0.15), residues: 1503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP E 261 
 HIS   0.005   0.001   HIS C 367 
 PHE   0.014   0.002   PHE C 256 
 TYR   0.017   0.002   TYR D 442 
 ARG   0.010   0.001   ARG B  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03185 (  252)
  hydrogen bonds       : angle       5.87328 (  642)
  SS BOND              : bond        0.00457 (    2)
  SS BOND              : angle       0.93264 (    4)
  covalent geometry    : bond        0.00283 (18730)
  covalent geometry    : angle       0.59533 (25485)

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

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

  4606 Ramachandran restraints generated.
    2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4606 Ramachandran restraints generated.
    2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 92
  time to evaluate  : 1.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 MET cc_start: 0.3555 (pmm) cc_final: 0.1254 (mpp)
REVERT: A  282 MET cc_start: 0.0539 (tmt) cc_final: -0.2679 (mmt)
REVERT: A  371 TYR cc_start: 0.3308 (m-80) cc_final: 0.2147 (m-80)
REVERT: B  255 LEU cc_start: 0.2685 (OUTLIER) cc_final: 0.2457 (pp)
REVERT: B  330 PHE cc_start: 0.3505 (m-80) cc_final: 0.2841 (m-80)
REVERT: B  369 GLU cc_start: 0.2373 (tp30) cc_final: 0.1858 (tp30)
REVERT: B  389 MET cc_start: 0.1106 (ttt) cc_final: -0.0423 (pp-130)
REVERT: D  366 ARG cc_start: 0.2941 (mmt-90) cc_final: 0.0480 (ttm110)
REVERT: D  395 MET cc_start: 0.0330 (ptm) cc_final: -0.2444 (tmm)
REVERT: E  246 MET cc_start: 0.1008 (OUTLIER) cc_final: -0.0175 (tmm)
REVERT: E  247 PHE cc_start: 0.2768 (OUTLIER) cc_final: 0.2062 (p90)
REVERT: E  282 MET cc_start: 0.2015 (tmt) cc_final: 0.0266 (mmp)
REVERT: E  319 HIS cc_start: 0.1548 (m-70) cc_final: 0.1170 (m-70)
REVERT: E  350 SER cc_start: 0.5724 (OUTLIER) cc_final: 0.5121 (m)
REVERT: E  360 LYS cc_start: -0.0490 (OUTLIER) cc_final: -0.0811 (mmtm)
REVERT: E  467 ARG cc_start: 0.3198 (mtt90) cc_final: 0.0159 (tpt-90)
REVERT: C  255 LEU cc_start: 0.3670 (OUTLIER) cc_final: 0.3309 (pp)
REVERT: C  389 MET cc_start: -0.2140 (OUTLIER) cc_final: -0.2694 (mmm)
  outliers start: 57
  outliers final: 41
  residues processed: 135
  average time/residue: 0.9082
  time to fit residues: 145.5743
Evaluate side-chains
  133 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 85
  time to evaluate  : 1.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 ASN
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   73 PHE
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 CYS
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain B residue   50 PHE
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain B residue  200 MET
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  327 ASN
Chi-restraints excluded: chain B residue  375 PHE
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue  129 THR
Chi-restraints excluded: chain D residue  130 GLU
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  267 MET
Chi-restraints excluded: chain D residue  333 VAL
Chi-restraints excluded: chain D residue  452 LEU
Chi-restraints excluded: chain E residue   45 VAL
Chi-restraints excluded: chain E residue   99 VAL
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  202 ASP
Chi-restraints excluded: chain E residue  246 MET
Chi-restraints excluded: chain E residue  247 PHE
Chi-restraints excluded: chain E residue  256 PHE
Chi-restraints excluded: chain E residue  333 VAL
Chi-restraints excluded: chain E residue  350 SER
Chi-restraints excluded: chain E residue  360 LYS
Chi-restraints excluded: chain E residue  375 PHE
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  120 HIS
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  267 MET
Chi-restraints excluded: chain C residue  294 SER
Chi-restraints excluded: chain C residue  389 MET
Chi-restraints excluded: chain C residue  450 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 127 optimal weight:    1.9990
   chunk 140 optimal weight:    0.8980
   chunk 169 optimal weight:    0.8980
   chunk 111 optimal weight:    0.7980
   chunk 215 optimal weight:    0.9990
   chunk 89 optimal weight:    0.4980
   chunk 14 optimal weight:   20.0000
   chunk 45 optimal weight:    0.5980
   chunk 113 optimal weight:    5.9990
   chunk 67 optimal weight:    0.0570
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
** L  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  92 ASN
** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 462 GLN
** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 367 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 = 0.5156 r_free = 0.5156 target = 0.309869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.5045 r_free = 0.5045 target = 0.293195 restraints weight = 24914.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.5070 rms_B_bonded: 1.78
r_work: 0.5009 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.4914 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.4914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1512
moved from start:          0.6445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  18732  Z= 0.100
  Angle     :  0.544   8.856  25489  Z= 0.274
  Chirality :  0.043   0.197   2753
  Planarity :  0.004   0.045   3323
  Dihedral  :  4.745  20.630   2527
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 14.90 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.17), residues: 2303
  helix: -0.50 (0.36), residues: 199
  sheet: -1.07 (0.21), residues: 609
  loop : -1.12 (0.15), residues: 1495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP E 261 
 HIS   0.003   0.001   HIS B 168 
 PHE   0.015   0.001   PHE B 248 
 TYR   0.019   0.001   TYR B 371 
 ARG   0.006   0.000   ARG B  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02877 (  252)
  hydrogen bonds       : angle       5.53077 (  642)
  SS BOND              : bond        0.00362 (    2)
  SS BOND              : angle       0.84709 (    4)
  covalent geometry    : bond        0.00229 (18730)
  covalent geometry    : angle       0.54405 (25485)

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

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

  4606 Ramachandran restraints generated.
    2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4606 Ramachandran restraints generated.
    2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 86
  time to evaluate  : 1.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 MET cc_start: 0.3350 (pmm) cc_final: 0.1279 (mpp)
REVERT: A  282 MET cc_start: 0.0304 (tmt) cc_final: -0.2720 (mmt)
REVERT: A  371 TYR cc_start: 0.3095 (m-80) cc_final: 0.2092 (m-80)
REVERT: B  255 LEU cc_start: 0.2564 (OUTLIER) cc_final: 0.2299 (pp)
REVERT: B  330 PHE cc_start: 0.3234 (m-80) cc_final: 0.2582 (m-80)
REVERT: B  369 GLU cc_start: 0.2241 (tp30) cc_final: 0.1870 (tp30)
REVERT: B  374 GLN cc_start: 0.5520 (tt0) cc_final: 0.4956 (tt0)
REVERT: B  389 MET cc_start: 0.1230 (ttt) cc_final: -0.0419 (pp-130)
REVERT: D  129 THR cc_start: 0.2307 (OUTLIER) cc_final: 0.1999 (t)
REVERT: D  366 ARG cc_start: 0.2904 (mmt-90) cc_final: 0.0541 (ttm110)
REVERT: D  395 MET cc_start: 0.0275 (ptm) cc_final: -0.2093 (tmm)
REVERT: E  247 PHE cc_start: 0.2652 (OUTLIER) cc_final: 0.1891 (p90)
REVERT: E  282 MET cc_start: 0.1831 (tmt) cc_final: 0.0140 (mmp)
REVERT: E  319 HIS cc_start: 0.1484 (m-70) cc_final: 0.1130 (m-70)
REVERT: E  350 SER cc_start: 0.5538 (OUTLIER) cc_final: 0.4852 (m)
REVERT: E  467 ARG cc_start: 0.2932 (mtt90) cc_final: 0.0289 (tpp80)
REVERT: C  255 LEU cc_start: 0.3372 (OUTLIER) cc_final: 0.3123 (pp)
REVERT: C  389 MET cc_start: -0.1967 (OUTLIER) cc_final: -0.2504 (mmm)
  outliers start: 47
  outliers final: 34
  residues processed: 122
  average time/residue: 0.9482
  time to fit residues: 136.6223
Evaluate side-chains
  125 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 85
  time to evaluate  : 1.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 ASN
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   73 PHE
Chi-restraints excluded: chain A residue  133 HIS
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  365 SER
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain B residue  200 MET
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  375 PHE
Chi-restraints excluded: chain B residue  442 TYR
Chi-restraints excluded: chain D residue  129 THR
Chi-restraints excluded: chain D residue  267 MET
Chi-restraints excluded: chain D residue  333 VAL
Chi-restraints excluded: chain D residue  452 LEU
Chi-restraints excluded: chain E residue   45 VAL
Chi-restraints excluded: chain E residue   73 PHE
Chi-restraints excluded: chain E residue   99 VAL
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  202 ASP
Chi-restraints excluded: chain E residue  247 PHE
Chi-restraints excluded: chain E residue  256 PHE
Chi-restraints excluded: chain E residue  333 VAL
Chi-restraints excluded: chain E residue  350 SER
Chi-restraints excluded: chain E residue  375 PHE
Chi-restraints excluded: chain E residue  400 LEU
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  120 HIS
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  267 MET
Chi-restraints excluded: chain C residue  294 SER
Chi-restraints excluded: chain C residue  389 MET
Chi-restraints excluded: chain C residue  450 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 13 optimal weight:   20.0000
   chunk 167 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 225 optimal weight:    0.9980
   chunk 159 optimal weight:    7.9990
   chunk 190 optimal weight:    2.9990
   chunk 144 optimal weight:    0.0970
   chunk 72 optimal weight:    8.9990
   chunk 124 optimal weight:    5.9990
   chunk 123 optimal weight:    0.9980
   overall best weight:    1.1580

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

Flipped N/Q/H residues before XYZ refinement:
H  94 HIS
L  32 ASN
** L  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  92 ASN
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 124 ASN
** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 111 GLN
E 153 GLN
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 367 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 = 0.5153 r_free = 0.5153 target = 0.309964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.5023 r_free = 0.5023 target = 0.292493 restraints weight = 25174.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.5031 rms_B_bonded: 1.90
r_work: 0.4981 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.4882 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.4882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1703
moved from start:          0.6929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  18732  Z= 0.136
  Angle     :  0.610  10.261  25489  Z= 0.309
  Chirality :  0.045   0.237   2753
  Planarity :  0.004   0.049   3323
  Dihedral  :  5.005  23.851   2527
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 16.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 14.76 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.17), residues: 2303
  helix: -0.31 (0.37), residues: 191
  sheet: -1.12 (0.21), residues: 611
  loop : -1.23 (0.15), residues: 1501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP E 261 
 HIS   0.006   0.001   HIS C 367 
 PHE   0.015   0.002   PHE B 361 
 TYR   0.019   0.002   TYR B 371 
 ARG   0.005   0.001   ARG B  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03145 (  252)
  hydrogen bonds       : angle       5.79500 (  642)
  SS BOND              : bond        0.00576 (    2)
  SS BOND              : angle       1.23980 (    4)
  covalent geometry    : bond        0.00307 (18730)
  covalent geometry    : angle       0.60981 (25485)

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

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

  4606 Ramachandran restraints generated.
    2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4606 Ramachandran restraints generated.
    2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 89
  time to evaluate  : 2.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 MET cc_start: 0.3535 (pmm) cc_final: 0.1477 (mpp)
REVERT: A  282 MET cc_start: 0.0263 (tmt) cc_final: -0.2560 (mmt)
REVERT: A  371 TYR cc_start: 0.3371 (m-80) cc_final: 0.2197 (m-80)
REVERT: B  246 MET cc_start: 0.3374 (OUTLIER) cc_final: 0.3091 (mtp)
REVERT: B  330 PHE cc_start: 0.3718 (m-80) cc_final: 0.2941 (m-80)
REVERT: B  369 GLU cc_start: 0.2397 (tp30) cc_final: 0.1876 (tp30)
REVERT: B  374 GLN cc_start: 0.5384 (OUTLIER) cc_final: 0.4750 (tt0)
REVERT: B  389 MET cc_start: 0.1294 (ttt) cc_final: -0.0511 (pp-130)
REVERT: D  366 ARG cc_start: 0.3116 (mmt-90) cc_final: 0.0784 (ttm110)
REVERT: D  395 MET cc_start: 0.0443 (ptm) cc_final: -0.2273 (tmm)
REVERT: E  125 LYS cc_start: -0.0986 (OUTLIER) cc_final: -0.1636 (ptmm)
REVERT: E  237 MET cc_start: 0.1494 (mmm) cc_final: 0.0709 (mmm)
REVERT: E  247 PHE cc_start: 0.3032 (OUTLIER) cc_final: 0.2212 (p90)
REVERT: E  282 MET cc_start: 0.1823 (tmt) cc_final: 0.0239 (mmp)
REVERT: E  319 HIS cc_start: 0.1622 (m-70) cc_final: 0.1277 (m-70)
REVERT: E  360 LYS cc_start: -0.0418 (OUTLIER) cc_final: -0.0769 (mmtt)
REVERT: E  467 ARG cc_start: 0.3087 (mtt90) cc_final: 0.0319 (tpp80)
REVERT: C  255 LEU cc_start: 0.3642 (OUTLIER) cc_final: 0.3240 (pp)
REVERT: C  389 MET cc_start: -0.2003 (mmm) cc_final: -0.2545 (mmm)
  outliers start: 56
  outliers final: 45
  residues processed: 133
  average time/residue: 0.9206
  time to fit residues: 146.3984
Evaluate side-chains
  140 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 89
  time to evaluate  : 1.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 ASN
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   73 PHE
Chi-restraints excluded: chain A residue  133 HIS
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  365 SER
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain B residue   92 ASN
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain B residue  200 MET
Chi-restraints excluded: chain B residue  246 MET
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  374 GLN
Chi-restraints excluded: chain B residue  375 PHE
Chi-restraints excluded: chain B residue  442 TYR
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue  129 THR
Chi-restraints excluded: chain D residue  267 MET
Chi-restraints excluded: chain D residue  333 VAL
Chi-restraints excluded: chain D residue  452 LEU
Chi-restraints excluded: chain E residue   45 VAL
Chi-restraints excluded: chain E residue   73 PHE
Chi-restraints excluded: chain E residue   99 VAL
Chi-restraints excluded: chain E residue  125 LYS
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  202 ASP
Chi-restraints excluded: chain E residue  242 TYR
Chi-restraints excluded: chain E residue  247 PHE
Chi-restraints excluded: chain E residue  256 PHE
Chi-restraints excluded: chain E residue  333 VAL
Chi-restraints excluded: chain E residue  360 LYS
Chi-restraints excluded: chain E residue  375 PHE
Chi-restraints excluded: chain E residue  400 LEU
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  120 HIS
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  267 MET
Chi-restraints excluded: chain C residue  294 SER
Chi-restraints excluded: chain C residue  301 THR
Chi-restraints excluded: chain C residue  450 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0000
   chunk 11 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 13 optimal weight:    8.9990
   chunk 174 optimal weight:    6.9990
   chunk 207 optimal weight:    0.4980
   chunk 149 optimal weight:    0.0970
   chunk 210 optimal weight:    0.7980
   chunk 191 optimal weight:    9.9990
   chunk 170 optimal weight:    0.8980
   overall best weight:    0.4582

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

Flipped N/Q/H residues before XYZ refinement:
H   5 GLN
H  94 HIS
** L  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  92 ASN
** B  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 133 HIS
** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 319 HIS
** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 HIS
** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 367 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 = 0.5185 r_free = 0.5185 target = 0.312788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.5053 r_free = 0.5053 target = 0.295141 restraints weight = 24775.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.5033 rms_B_bonded: 1.85
r_work: 0.4985 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.4888 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.4888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1563
moved from start:          0.6922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  18732  Z= 0.097
  Angle     :  0.563  15.207  25489  Z= 0.279
  Chirality :  0.043   0.182   2753
  Planarity :  0.004   0.046   3323
  Dihedral  :  4.641  20.447   2527
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.20 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.17), residues: 2303
  helix: -0.13 (0.37), residues: 191
  sheet: -1.09 (0.21), residues: 600
  loop : -1.07 (0.15), residues: 1512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP E 261 
 HIS   0.004   0.001   HIS D 326 
 PHE   0.014   0.001   PHE B 248 
 TYR   0.027   0.001   TYR D 442 
 ARG   0.005   0.000   ARG B  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02885 (  252)
  hydrogen bonds       : angle       5.49685 (  642)
  SS BOND              : bond        0.00419 (    2)
  SS BOND              : angle       0.86475 (    4)
  covalent geometry    : bond        0.00220 (18730)
  covalent geometry    : angle       0.56274 (25485)

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

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

  4606 Ramachandran restraints generated.
    2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4606 Ramachandran restraints generated.
    2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 88
  time to evaluate  : 1.868 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 MET cc_start: 0.3475 (pmm) cc_final: 0.1457 (mpp)
REVERT: A  282 MET cc_start: 0.0134 (tmt) cc_final: -0.2604 (mmt)
REVERT: A  371 TYR cc_start: 0.2966 (m-80) cc_final: 0.2024 (m-80)
REVERT: B  246 MET cc_start: 0.2845 (mtp) cc_final: 0.2589 (mtp)
REVERT: B  330 PHE cc_start: 0.3309 (m-80) cc_final: 0.2600 (m-80)
REVERT: B  369 GLU cc_start: 0.2330 (tp30) cc_final: 0.2001 (tp30)
REVERT: B  374 GLN cc_start: 0.5419 (OUTLIER) cc_final: 0.4951 (tm-30)
REVERT: B  389 MET cc_start: 0.1134 (ttt) cc_final: -0.0687 (pp-130)
REVERT: D  129 THR cc_start: 0.2115 (OUTLIER) cc_final: 0.1908 (t)
REVERT: D  237 MET cc_start: 0.0869 (mpt) cc_final: 0.0375 (mtm)
REVERT: D  366 ARG cc_start: 0.2830 (mmt-90) cc_final: 0.0613 (ttm110)
REVERT: D  395 MET cc_start: 0.0159 (ptm) cc_final: -0.2093 (tmm)
REVERT: E  247 PHE cc_start: 0.2679 (OUTLIER) cc_final: 0.1777 (p90)
REVERT: E  282 MET cc_start: 0.1553 (tmt) cc_final: 0.0213 (mmp)
REVERT: E  319 HIS cc_start: 0.1487 (m-70) cc_final: 0.1181 (m-70)
REVERT: E  467 ARG cc_start: 0.2983 (mtt90) cc_final: 0.0180 (tpp80)
REVERT: C  389 MET cc_start: -0.1919 (mmm) cc_final: -0.2503 (mmm)
  outliers start: 47
  outliers final: 38
  residues processed: 124
  average time/residue: 0.8664
  time to fit residues: 128.7873
Evaluate side-chains
  127 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 86
  time to evaluate  : 1.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 ASN
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   73 PHE
Chi-restraints excluded: chain A residue  133 HIS
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain B residue  200 MET
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  374 GLN
Chi-restraints excluded: chain B residue  375 PHE
Chi-restraints excluded: chain B residue  442 TYR
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue  129 THR
Chi-restraints excluded: chain D residue  267 MET
Chi-restraints excluded: chain D residue  452 LEU
Chi-restraints excluded: chain E residue   45 VAL
Chi-restraints excluded: chain E residue   73 PHE
Chi-restraints excluded: chain E residue   99 VAL
Chi-restraints excluded: chain E residue  125 LYS
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  202 ASP
Chi-restraints excluded: chain E residue  247 PHE
Chi-restraints excluded: chain E residue  256 PHE
Chi-restraints excluded: chain E residue  333 VAL
Chi-restraints excluded: chain E residue  375 PHE
Chi-restraints excluded: chain E residue  400 LEU
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  120 HIS
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  267 MET
Chi-restraints excluded: chain C residue  294 SER
Chi-restraints excluded: chain C residue  301 THR
Chi-restraints excluded: chain C residue  450 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 89 optimal weight:    0.6980
   chunk 125 optimal weight:    4.9990
   chunk 105 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   chunk 53 optimal weight:    0.8980
   chunk 145 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   chunk 168 optimal weight:    2.9990
   chunk 212 optimal weight:    0.7980
   chunk 133 optimal weight:    9.9990
   chunk 182 optimal weight:    7.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
H  94 HIS
** L  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  76 GLN
B  92 ASN
** B  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 138 ASN
** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 341 ASN
** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 273 GLN
E 317 GLN
E 341 ASN
** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5158 r_free = 0.5158 target = 0.310232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.5038 r_free = 0.5038 target = 0.293684 restraints weight = 25303.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.5077 rms_B_bonded: 1.88
r_work: 0.5025 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.4928 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.4928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1918
moved from start:          0.7784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  18732  Z= 0.178
  Angle     :  0.714  11.243  25489  Z= 0.363
  Chirality :  0.048   0.290   2753
  Planarity :  0.005   0.051   3323
  Dihedral  :  5.533  25.643   2527
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 19.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 14.90 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.16), residues: 2303
  helix: -0.27 (0.37), residues: 183
  sheet: -1.35 (0.21), residues: 565
  loop : -1.31 (0.15), residues: 1555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E 261 
 HIS   0.010   0.002   HIS E 259 
 PHE   0.021   0.002   PHE B 307 
 TYR   0.032   0.002   TYR D 442 
 ARG   0.007   0.001   ARG E 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03645 (  252)
  hydrogen bonds       : angle       6.28409 (  642)
  SS BOND              : bond        0.00877 (    2)
  SS BOND              : angle       1.96216 (    4)
  covalent geometry    : bond        0.00404 (18730)
  covalent geometry    : angle       0.71325 (25485)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10728.91 seconds
wall clock time: 186 minutes 11.38 seconds (11171.38 seconds total)