Starting phenix.real_space_refine
on Thu Feb  5 01:30:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ipq_35640/02_2026/8ipq_35640.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ipq_35640/02_2026/8ipq_35640.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ipq_35640/02_2026/8ipq_35640.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ipq_35640/02_2026/8ipq_35640.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ipq_35640/02_2026/8ipq_35640.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ipq_35640/02_2026/8ipq_35640.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.060
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      58      5.16       5
     C    9180      2.51       5
     N    2608      2.21       5
     O    2610      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14456
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 3679
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 3679
          Classifications: {'peptide': 505}
          Link IDs: {'PTRANS': 31, 'TRANS': 473}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 3549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 493, 3549
          Classifications: {'peptide': 493}
          Link IDs: {'PTRANS': 29, 'TRANS': 463}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3679
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 3679
          Classifications: {'peptide': 505}
          Link IDs: {'PTRANS': 31, 'TRANS': 473}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 3549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 493, 3549
          Classifications: {'peptide': 493}
          Link IDs: {'PTRANS': 29, 'TRANS': 463}
          Chain breaks: 1
  Time building chain proxies: 3.51, per 1000 atoms: 0.24
  Number of scatterers: 14456
  At special positions: 0
  Unit cell: (89.024, 137.28, 188.032, 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      58     16.00
     O    2610      8.00
     N    2608      7.00
     C    9180      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.35
  Conformation dependent library (CDL) restraints added in 527.9 milliseconds
  

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3644

  Finding SS restraints...
    Secondary structure from input PDB file:
      92 helices and 8 sheets defined
      70.6% alpha, 3.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'B' and resid -5 through 24
      removed outlier: 3.584A  pdb=" N   SER B  10 " --> pdb=" O   CYS B   6 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ASN B  24 " --> pdb=" O   GLY B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 80
      removed outlier: 3.603A  pdb=" N   GLY B  38 " --> pdb=" O   ASP B  34 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU B  39 " --> pdb=" O   TRP B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 98
      removed outlier: 3.908A  pdb=" N   LEU B  87 " --> pdb=" O   SER B  83 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ALA B  89 " --> pdb=" O   ARG B  85 " (cutoff:3.500A)
      removed outlier: 5.786A  pdb=" N   ASP B  92 " --> pdb=" O   ALA B  88 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   SER B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 104
      No H-bonds generated for 'chain 'B' and resid 102 through 104'
    Processing helix  chain 'B' and resid 105 through 112
      removed outlier: 3.731A  pdb=" N   TYR B 112 " --> pdb=" O   TYR B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 134
      removed outlier: 3.802A  pdb=" N   THR B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
      Proline residue:  B 124  - end of helix
    Processing helix  chain 'B' and resid 134 through 145
      removed outlier: 3.623A  pdb=" N   ALA B 138 " --> pdb=" O   ASP B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 159
    Processing helix  chain 'B' and resid 161 through 183
      removed outlier: 3.657A  pdb=" N   ALA B 165 " --> pdb=" O   GLU B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 189
      removed outlier: 3.684A  pdb=" N   ALA B 189 " --> pdb=" O   PRO B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 219
      removed outlier: 3.594A  pdb=" N   ILE B 200 " --> pdb=" O   SER B 196 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ALA B 201 " --> pdb=" O   VAL B 197 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   GLU B 202 " --> pdb=" O   GLN B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 245
      removed outlier: 4.126A  pdb=" N   VAL B 233 " --> pdb=" O   ALA B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 276
      Proline residue:  B 262  - end of helix
      Proline residue:  B 267  - end of helix
      removed outlier: 4.311A  pdb=" N   HIS B 276 " --> pdb=" O   GLY B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 290
    Processing helix  chain 'B' and resid 335 through 344
    Processing helix  chain 'B' and resid 362 through 364
      No H-bonds generated for 'chain 'B' and resid 362 through 364'
    Processing helix  chain 'B' and resid 365 through 371
      removed outlier: 3.712A  pdb=" N   GLY B 371 " --> pdb=" O   SER B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 391
    Processing helix  chain 'B' and resid 399 through 408
    Processing helix  chain 'B' and resid 409 through 416
      removed outlier: 3.585A  pdb=" N   GLU B 415 " --> pdb=" O   GLU B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 446
      removed outlier: 3.679A  pdb=" N   GLY B 446 " --> pdb=" O   VAL B 442 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 462 through 479
    Processing helix  chain 'B' and resid 489 through 494
    Processing helix  chain 'A' and resid 7 through 16
    Processing helix  chain 'A' and resid 20 through 54
      removed outlier: 3.877A  pdb=" N   PHE A  24 " --> pdb=" O   ARG A  20 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA A  27 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLN A  54 " --> pdb=" O   THR A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 105
      removed outlier: 4.225A  pdb=" N   VAL A  63 " --> pdb=" O   LEU A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 126
    Processing helix  chain 'A' and resid 126 through 135
      removed outlier: 3.588A  pdb=" N   ASP A 130 " --> pdb=" O   GLY A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 161
      removed outlier: 3.732A  pdb=" N   VAL A 156 " --> pdb=" O   ALA A 152 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ILE A 157 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ILE A 160 " --> pdb=" O   VAL A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 193
      Proline residue:  A 180  - end of helix
      removed outlier: 3.538A  pdb=" N   THR A 192 " --> pdb=" O   HIS A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
      removed outlier: 3.849A  pdb=" N   ASP A 202 " --> pdb=" O   ARG A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 218
      removed outlier: 4.095A  pdb=" N   SER A 218 " --> pdb=" O   GLU A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 244
      removed outlier: 4.137A  pdb=" N   HIS A 231 " --> pdb=" O   THR A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 270
      removed outlier: 4.341A  pdb=" N   VAL A 248 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ALA A 249 " --> pdb=" O   PRO A 245 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
      removed outlier: 3.648A  pdb=" N   ALA A 270 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 286
    Processing helix  chain 'A' and resid 287 through 290
    Processing helix  chain 'A' and resid 293 through 297
    Processing helix  chain 'A' and resid 299 through 317
      removed outlier: 3.679A  pdb=" N   LEU A 317 " --> pdb=" O   ARG A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 363
    Processing helix  chain 'A' and resid 385 through 391
    Processing helix  chain 'A' and resid 398 through 410
    Processing helix  chain 'A' and resid 411 through 417
    Processing helix  chain 'A' and resid 420 through 424
      removed outlier: 3.783A  pdb=" N   THR A 424 " --> pdb=" O   GLY A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 433
      removed outlier: 3.538A  pdb=" N   ALA A 431 " --> pdb=" O   GLY A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 449
    Processing helix  chain 'A' and resid 467 through 477
    Processing helix  chain 'C' and resid -4 through 24
      removed outlier: 3.584A  pdb=" N   SER C  10 " --> pdb=" O   CYS C   6 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ASN C  24 " --> pdb=" O   GLY C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 34 through 80
      removed outlier: 3.604A  pdb=" N   GLY C  38 " --> pdb=" O   ASP C  34 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU C  39 " --> pdb=" O   TRP C  35 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 83 through 98
      removed outlier: 3.908A  pdb=" N   LEU C  87 " --> pdb=" O   SER C  83 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ALA C  89 " --> pdb=" O   ARG C  85 " (cutoff:3.500A)
      removed outlier: 5.786A  pdb=" N   ASP C  92 " --> pdb=" O   ALA C  88 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   SER C  93 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 104
      No H-bonds generated for 'chain 'C' and resid 102 through 104'
    Processing helix  chain 'C' and resid 105 through 112
      removed outlier: 3.731A  pdb=" N   TYR C 112 " --> pdb=" O   TYR C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 134
      removed outlier: 3.802A  pdb=" N   THR C 123 " --> pdb=" O   ALA C 119 " (cutoff:3.500A)
      Proline residue:  C 124  - end of helix
    Processing helix  chain 'C' and resid 134 through 145
      removed outlier: 3.622A  pdb=" N   ALA C 138 " --> pdb=" O   ASP C 134 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 147 through 159
    Processing helix  chain 'C' and resid 161 through 183
      removed outlier: 3.657A  pdb=" N   ALA C 165 " --> pdb=" O   GLU C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 189
      removed outlier: 3.684A  pdb=" N   ALA C 189 " --> pdb=" O   PRO C 185 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 219
      removed outlier: 3.594A  pdb=" N   ILE C 200 " --> pdb=" O   SER C 196 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ALA C 201 " --> pdb=" O   VAL C 197 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   GLU C 202 " --> pdb=" O   GLN C 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 219 through 245
      removed outlier: 4.125A  pdb=" N   VAL C 233 " --> pdb=" O   ALA C 229 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 276
      Proline residue:  C 262  - end of helix
      Proline residue:  C 267  - end of helix
      removed outlier: 4.310A  pdb=" N   HIS C 276 " --> pdb=" O   GLY C 272 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 278 through 290
    Processing helix  chain 'C' and resid 335 through 344
    Processing helix  chain 'C' and resid 362 through 364
      No H-bonds generated for 'chain 'C' and resid 362 through 364'
    Processing helix  chain 'C' and resid 365 through 371
      removed outlier: 3.713A  pdb=" N   GLY C 371 " --> pdb=" O   SER C 367 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 387 through 391
    Processing helix  chain 'C' and resid 399 through 408
    Processing helix  chain 'C' and resid 409 through 416
      removed outlier: 3.585A  pdb=" N   GLU C 415 " --> pdb=" O   GLU C 411 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 432 through 446
      removed outlier: 3.680A  pdb=" N   GLY C 446 " --> pdb=" O   VAL C 442 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 462 through 479
    Processing helix  chain 'C' and resid 489 through 494
    Processing helix  chain 'D' and resid 7 through 16
    Processing helix  chain 'D' and resid 20 through 54
      removed outlier: 3.877A  pdb=" N   PHE D  24 " --> pdb=" O   ARG D  20 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ALA D  27 " --> pdb=" O   ARG D  23 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLN D  54 " --> pdb=" O   THR D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 59 through 105
      removed outlier: 4.225A  pdb=" N   VAL D  63 " --> pdb=" O   LEU D  59 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 117 through 126
    Processing helix  chain 'D' and resid 126 through 135
      removed outlier: 3.588A  pdb=" N   ASP D 130 " --> pdb=" O   GLY D 126 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 140 through 161
      removed outlier: 3.732A  pdb=" N   VAL D 156 " --> pdb=" O   ALA D 152 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ILE D 157 " --> pdb=" O   ALA D 153 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ILE D 160 " --> pdb=" O   VAL D 156 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 164 through 193
      Proline residue:  D 180  - end of helix
      removed outlier: 3.538A  pdb=" N   THR D 192 " --> pdb=" O   HIS D 188 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 205
      removed outlier: 3.849A  pdb=" N   ASP D 202 " --> pdb=" O   ARG D 198 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 211 through 218
      removed outlier: 4.095A  pdb=" N   SER D 218 " --> pdb=" O   GLU D 214 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 220 through 244
      removed outlier: 4.137A  pdb=" N   HIS D 231 " --> pdb=" O   THR D 227 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 244 through 270
      removed outlier: 4.342A  pdb=" N   VAL D 248 " --> pdb=" O   ALA D 244 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ALA D 249 " --> pdb=" O   PRO D 245 " (cutoff:3.500A)
      Proline residue:  D 253  - end of helix
      removed outlier: 3.648A  pdb=" N   ALA D 270 " --> pdb=" O   ILE D 266 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 276 through 286
    Processing helix  chain 'D' and resid 287 through 290
    Processing helix  chain 'D' and resid 293 through 297
    Processing helix  chain 'D' and resid 299 through 317
      removed outlier: 3.678A  pdb=" N   LEU D 317 " --> pdb=" O   ARG D 313 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 349 through 363
    Processing helix  chain 'D' and resid 385 through 391
    Processing helix  chain 'D' and resid 398 through 410
    Processing helix  chain 'D' and resid 411 through 417
    Processing helix  chain 'D' and resid 420 through 424
      removed outlier: 3.783A  pdb=" N   THR D 424 " --> pdb=" O   GLY D 421 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 428 through 433
      removed outlier: 3.538A  pdb=" N   ALA D 431 " --> pdb=" O   GLY D 428 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 434 through 449
    Processing helix  chain 'D' and resid 467 through 477
    Processing sheet with id=AA1, first strand: chain 'B' and resid 318 through 320
      removed outlier: 3.549A  pdb=" N   LEU B 355 " --> pdb=" O   GLU B 312 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 373 through 376
      removed outlier: 3.518A  pdb=" N   LEU B 453 " --> pdb=" O   ALA B 374 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   VAL B 325 " --> pdb=" O   HIS B 498 " (cutoff:3.500A)
      removed outlier: 8.308A  pdb=" N   VAL B 500 " --> pdb=" O   VAL B 325 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   VAL B 327 " --> pdb=" O   VAL B 500 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 385 through 386
    Processing sheet with id=AA4, first strand: chain 'A' and resid 339 through 340
      removed outlier: 3.503A  pdb=" N   LEU A 455 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 318 through 320
      removed outlier: 3.549A  pdb=" N   LEU C 355 " --> pdb=" O   GLU C 312 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 373 through 376
      removed outlier: 3.518A  pdb=" N   LEU C 453 " --> pdb=" O   ALA C 374 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   VAL C 325 " --> pdb=" O   HIS C 498 " (cutoff:3.500A)
      removed outlier: 8.308A  pdb=" N   VAL C 500 " --> pdb=" O   VAL C 325 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL C 327 " --> pdb=" O   VAL C 500 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 385 through 386
    Processing sheet with id=AA8, first strand: chain 'D' and resid 339 through 340
      removed outlier: 3.504A  pdb=" N   LEU D 455 " --> pdb=" O   ALA D 373 " (cutoff:3.500A)

    994 hydrogen bonds defined for protein.
    2922 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: 2.53

  Time building geometry restraints manager: 1.73 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2978
        1.33 -     1.45: 2963
        1.45 -     1.58: 8661
        1.58 -     1.70: 0
        1.70 -     1.82: 98
  Bond restraints: 14700
  Sorted by residual:
  bond pdb=" C   GLU C 294 "
       pdb=" N   PRO C 295 "
    ideal  model  delta    sigma   weight residual
    1.331  1.389 -0.057 1.20e-02 6.94e+03 2.30e+01
  bond pdb=" C   GLU B 294 "
       pdb=" N   PRO B 295 "
    ideal  model  delta    sigma   weight residual
    1.331  1.389 -0.057 1.20e-02 6.94e+03 2.29e+01
  bond pdb=" CA  GLU B 456 "
       pdb=" C   GLU B 456 "
    ideal  model  delta    sigma   weight residual
    1.524  1.570 -0.046 1.26e-02 6.30e+03 1.32e+01
  bond pdb=" C   GLU B 456 "
       pdb=" N   PRO B 457 "
    ideal  model  delta    sigma   weight residual
    1.336  1.380 -0.044 1.25e-02 6.40e+03 1.26e+01
  bond pdb=" N   PHE C 219 "
       pdb=" CA  PHE C 219 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.26e-02 6.30e+03 7.37e+00
  ... (remaining 14695 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 19719
        2.26 -     4.52: 283
        4.52 -     6.78: 77
        6.78 -     9.04: 22
        9.04 -    11.30: 11
  Bond angle restraints: 20112
  Sorted by residual:
  angle pdb=" N   LEU C 344 "
        pdb=" CA  LEU C 344 "
        pdb=" C   LEU C 344 "
      ideal   model   delta    sigma   weight residual
     113.28  104.57    8.71 1.22e+00 6.72e-01 5.10e+01
  angle pdb=" N   LEU B 344 "
        pdb=" CA  LEU B 344 "
        pdb=" C   LEU B 344 "
      ideal   model   delta    sigma   weight residual
     113.28  104.58    8.70 1.22e+00 6.72e-01 5.09e+01
  angle pdb=" C   PHE C 219 "
        pdb=" CA  PHE C 219 "
        pdb=" CB  PHE C 219 "
      ideal   model   delta    sigma   weight residual
     110.56  101.08    9.48 1.69e+00 3.50e-01 3.15e+01
  angle pdb=" N   PRO C 295 "
        pdb=" CA  PRO C 295 "
        pdb=" C   PRO C 295 "
      ideal   model   delta    sigma   weight residual
     111.03  119.55   -8.52 1.54e+00 4.22e-01 3.06e+01
  angle pdb=" N   PRO B 295 "
        pdb=" CA  PRO B 295 "
        pdb=" C   PRO B 295 "
      ideal   model   delta    sigma   weight residual
     111.03  119.53   -8.50 1.54e+00 4.22e-01 3.05e+01
  ... (remaining 20107 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.21: 7632
       17.21 -    34.42: 942
       34.42 -    51.63: 260
       51.63 -    68.84: 20
       68.84 -    86.05: 10
  Dihedral angle restraints: 8864
    sinusoidal: 3220
      harmonic: 5644
  Sorted by residual:
  dihedral pdb=" C   THR B 299 "
           pdb=" N   THR B 299 "
           pdb=" CA  THR B 299 "
           pdb=" CB  THR B 299 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -134.61   12.61     0      2.50e+00 1.60e-01 2.55e+01
  dihedral pdb=" C   THR C 299 "
           pdb=" N   THR C 299 "
           pdb=" CA  THR C 299 "
           pdb=" CB  THR C 299 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -134.60   12.60     0      2.50e+00 1.60e-01 2.54e+01
  dihedral pdb=" N   THR B 299 "
           pdb=" C   THR B 299 "
           pdb=" CA  THR B 299 "
           pdb=" CB  THR B 299 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  135.58  -12.18     0      2.50e+00 1.60e-01 2.37e+01
  ... (remaining 8861 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.099: 2414
       0.099 -    0.198: 102
       0.198 -    0.296: 2
       0.296 -    0.395: 0
       0.395 -    0.494: 2
  Chirality restraints: 2520
  Sorted by residual:
  chirality pdb=" CA  THR B 299 "
            pdb=" N   THR B 299 "
            pdb=" C   THR B 299 "
            pdb=" CB  THR B 299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.03    0.49 2.00e-01 2.50e+01 6.10e+00
  chirality pdb=" CA  THR C 299 "
            pdb=" N   THR C 299 "
            pdb=" C   THR C 299 "
            pdb=" CB  THR C 299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.03    0.49 2.00e-01 2.50e+01 6.10e+00
  chirality pdb=" CA  PRO B 295 "
            pdb=" N   PRO B 295 "
            pdb=" C   PRO B 295 "
            pdb=" CB  PRO B 295 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 2517 not shown)

  Planarity restraints: 2588
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 343 "    0.016 2.00e-02 2.50e+03   3.34e-02 1.12e+01
        pdb=" C   ILE B 343 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   ILE B 343 "    0.022 2.00e-02 2.50e+03
        pdb=" N   LEU B 344 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C 343 "   -0.016 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" C   ILE C 343 "    0.058 2.00e-02 2.50e+03
        pdb=" O   ILE C 343 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   LEU C 344 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 126 "    0.044 5.00e-02 4.00e+02   6.69e-02 7.15e+00
        pdb=" N   PRO A 127 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 127 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 127 "    0.037 5.00e-02 4.00e+02
  ... (remaining 2585 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1903
        2.75 -     3.29: 14730
        3.29 -     3.82: 25155
        3.82 -     4.36: 26136
        4.36 -     4.90: 46398
  Nonbonded interactions: 114322
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 182 "
            pdb=" OG  SER A 118 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   LEU B 393 "
            pdb=" NE  ARG A 220 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" O   LEU C 393 "
            pdb=" NE  ARG D 220 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" OD1 ASP C 134 "
            pdb=" NH2 ARG C 243 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" OD1 ASP B 134 "
            pdb=" NH2 ARG B 243 "
     model   vdw
     2.243 3.120
  ... (remaining 114317 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.630
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
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   0.057  14700  Z= 0.200
  Angle     :  0.774  11.295  20112  Z= 0.393
  Chirality :  0.045   0.494   2520
  Planarity :  0.006   0.107   2588
  Dihedral  : 16.068  86.048   5220
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 16.79
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.17 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 28.28 %
    Favored  : 71.11 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.20), residues: 1980
  helix:  1.51 (0.15), residues: 1304
  sheet:  0.16 (0.52), residues: 120
  loop : -2.46 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  85 
 TYR   0.010   0.001   TYR B 133 
 PHE   0.016   0.001   PHE A  24 
 TRP   0.015   0.001   TRP C 375 
 HIS   0.005   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (14700)
  covalent geometry    : angle       0.77352 (20112)
  hydrogen bonds       : bond        0.14755 (  994)
  hydrogen bonds       : angle       4.92878 ( 2922)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 266
  time to evaluate  : 0.395 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   -4 TYR cc_start: 0.5522 (OUTLIER) cc_final: 0.5067 (t80)
REVERT: B  212 MET cc_start: 0.8675 (tpp) cc_final: 0.8415 (tpt)
REVERT: A  355 MET cc_start: 0.7854 (ptp) cc_final: 0.7559 (ptp)
REVERT: C   70 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7245 (tm-30)
REVERT: D  231 HIS cc_start: 0.7020 (m170) cc_final: 0.6575 (m170)
REVERT: D  299 ASP cc_start: 0.8494 (p0) cc_final: 0.6444 (t70)
REVERT: D  350 LYS cc_start: 0.5662 (mtpt) cc_final: 0.5346 (mptt)
REVERT: D  351 THR cc_start: 0.7983 (m) cc_final: 0.7361 (p)
REVERT: D  440 ARG cc_start: 0.9002 (mtt90) cc_final: 0.8723 (ttm170)
REVERT: D  456 LEU cc_start: 0.8556 (mm) cc_final: 0.8348 (mt)
  outliers start: 9
  outliers final: 1
  residues processed: 273
  average time/residue: 0.1357
  time to fit residues: 51.6222
Evaluate side-chains
  188 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 186
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   -4 TYR
Chi-restraints excluded: chain A residue  135 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 98 optimal weight:    0.0030
   chunk 194 optimal weight:    7.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    4.9990
   overall best weight:    0.6990

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

Flipped N/Q/H residues before XYZ refinement:
A  82 GLN
D  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.180916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.107255 restraints weight = 24401.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.110219 restraints weight = 11403.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.111987 restraints weight = 7425.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.112735 restraints weight = 6012.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 61)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.113297 restraints weight = 5480.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  14700  Z= 0.147
  Angle     :  0.720  12.093  20112  Z= 0.341
  Chirality :  0.042   0.266   2520
  Planarity :  0.006   0.063   2588
  Dihedral  :  4.398  48.339   2151
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.63 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 26.98 %
    Favored  : 69.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.20), residues: 1980
  helix:  1.57 (0.14), residues: 1318
  sheet: -0.03 (0.49), residues: 126
  loop : -2.58 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  86 
 TYR   0.018   0.001   TYR D 102 
 PHE   0.027   0.001   PHE C 409 
 TRP   0.022   0.001   TRP C 370 
 HIS   0.007   0.001   HIS D 380 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (14700)
  covalent geometry    : angle       0.72010 (20112)
  hydrogen bonds       : bond        0.05144 (  994)
  hydrogen bonds       : angle       4.27900 ( 2922)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 190
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   -4 TYR cc_start: 0.5411 (OUTLIER) cc_final: 0.4920 (t80)
REVERT: B  100 ARG cc_start: 0.7722 (mtt90) cc_final: 0.7422 (mpt180)
REVERT: B  170 MET cc_start: 0.8246 (ttp) cc_final: 0.7983 (ttm)
REVERT: B  376 MET cc_start: 0.8032 (tmm) cc_final: 0.7646 (tmm)
REVERT: A  211 HIS cc_start: 0.6698 (OUTLIER) cc_final: 0.6396 (t-170)
REVERT: A  305 MET cc_start: 0.8032 (mmm) cc_final: 0.7752 (mmt)
REVERT: C  376 MET cc_start: 0.7646 (tmm) cc_final: 0.7340 (tmm)
REVERT: C  390 ASN cc_start: 0.6739 (OUTLIER) cc_final: 0.6455 (m-40)
REVERT: C  451 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8442 (m)
REVERT: C  485 MET cc_start: 0.6623 (mpp) cc_final: 0.6126 (mmp)
REVERT: D  215 LEU cc_start: 0.9106 (tp) cc_final: 0.8658 (tp)
REVERT: D  220 ARG cc_start: 0.8691 (mmt180) cc_final: 0.8365 (mmt90)
REVERT: D  305 MET cc_start: 0.8076 (mmp) cc_final: 0.7834 (mmt)
REVERT: D  329 VAL cc_start: 0.2162 (OUTLIER) cc_final: 0.1250 (m)
REVERT: D  359 ASP cc_start: 0.8662 (t70) cc_final: 0.8247 (m-30)
REVERT: D  437 GLN cc_start: 0.8498 (mt0) cc_final: 0.7929 (pt0)
REVERT: D  440 ARG cc_start: 0.8892 (mtt90) cc_final: 0.8605 (ttm170)
  outliers start: 58
  outliers final: 24
  residues processed: 238
  average time/residue: 0.1160
  time to fit residues: 40.4674
Evaluate side-chains
  183 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 154
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   -4 TYR
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  211 HIS
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  228 PHE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  375 PHE
Chi-restraints excluded: chain C residue  320 MET
Chi-restraints excluded: chain C residue  373 LEU
Chi-restraints excluded: chain C residue  390 ASN
Chi-restraints excluded: chain C residue  422 THR
Chi-restraints excluded: chain C residue  439 LEU
Chi-restraints excluded: chain C residue  451 VAL
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   92 ARG
Chi-restraints excluded: chain D residue   99 THR
Chi-restraints excluded: chain D residue  228 PHE
Chi-restraints excluded: chain D residue  329 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 95 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 128 optimal weight:    0.9990
   chunk 180 optimal weight:    9.9990
   chunk 136 optimal weight:   10.0000
   chunk 93 optimal weight:   30.0000
   chunk 192 optimal weight:   10.0000
   chunk 129 optimal weight:    8.9990
   chunk 90 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0980
   overall best weight:    1.8188

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  56 GLN
D  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.177748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.105600 restraints weight = 24569.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.106034 restraints weight = 14662.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.105540 restraints weight = 9520.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.106155 restraints weight = 9308.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.106295 restraints weight = 7963.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  14700  Z= 0.172
  Angle     :  0.708  10.458  20112  Z= 0.338
  Chirality :  0.043   0.255   2520
  Planarity :  0.006   0.074   2588
  Dihedral  :  4.368  51.354   2151
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.32 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 27.12 %
    Favored  : 68.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.20), residues: 1980
  helix:  1.53 (0.15), residues: 1312
  sheet: -0.27 (0.50), residues: 122
  loop : -2.45 (0.27), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 115 
 TYR   0.017   0.002   TYR D 102 
 PHE   0.016   0.001   PHE D  24 
 TRP   0.018   0.001   TRP B 375 
 HIS   0.005   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (14700)
  covalent geometry    : angle       0.70753 (20112)
  hydrogen bonds       : bond        0.05079 (  994)
  hydrogen bonds       : angle       4.21929 ( 2922)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 161
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   -4 TYR cc_start: 0.5567 (OUTLIER) cc_final: 0.4898 (t80)
REVERT: B  170 MET cc_start: 0.8259 (ttp) cc_final: 0.7926 (ttm)
REVERT: B  376 MET cc_start: 0.7909 (tmm) cc_final: 0.7174 (tmm)
REVERT: A  211 HIS cc_start: 0.7137 (OUTLIER) cc_final: 0.6712 (t-170)
REVERT: C  336 LYS cc_start: 0.7101 (mttp) cc_final: 0.6493 (mttt)
REVERT: C  369 TRP cc_start: 0.6935 (t60) cc_final: 0.6669 (t60)
REVERT: C  390 ASN cc_start: 0.6685 (OUTLIER) cc_final: 0.6402 (m-40)
REVERT: C  409 PHE cc_start: 0.7784 (t80) cc_final: 0.7520 (t80)
REVERT: D   88 ASP cc_start: 0.9118 (OUTLIER) cc_final: 0.8506 (t70)
REVERT: D  220 ARG cc_start: 0.9043 (mmt180) cc_final: 0.8670 (mmt90)
REVERT: D  305 MET cc_start: 0.8193 (mmp) cc_final: 0.7888 (mmt)
REVERT: D  353 MET cc_start: 0.8069 (mmm) cc_final: 0.7852 (mmp)
REVERT: D  355 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6998 (ppp)
REVERT: D  359 ASP cc_start: 0.8792 (t70) cc_final: 0.8308 (m-30)
REVERT: D  380 HIS cc_start: 0.7172 (t70) cc_final: 0.6752 (t70)
REVERT: D  437 GLN cc_start: 0.8446 (mt0) cc_final: 0.7977 (pt0)
  outliers start: 65
  outliers final: 39
  residues processed: 214
  average time/residue: 0.1016
  time to fit residues: 32.6747
Evaluate side-chains
  194 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 150
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   -4 TYR
Chi-restraints excluded: chain B residue    1 VAL
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  369 TRP
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  460 HIS
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  211 HIS
Chi-restraints excluded: chain A residue  228 PHE
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  375 PHE
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  286 GLU
Chi-restraints excluded: chain C residue  320 MET
Chi-restraints excluded: chain C residue  390 ASN
Chi-restraints excluded: chain C residue  422 THR
Chi-restraints excluded: chain C residue  439 LEU
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain D residue   71 LEU
Chi-restraints excluded: chain D residue   88 ASP
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   92 ARG
Chi-restraints excluded: chain D residue   96 ASN
Chi-restraints excluded: chain D residue   99 THR
Chi-restraints excluded: chain D residue  173 VAL
Chi-restraints excluded: chain D residue  228 PHE
Chi-restraints excluded: chain D residue  355 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 173 optimal weight:    4.9990
   chunk 196 optimal weight:   20.0000
   chunk 90 optimal weight:   30.0000
   chunk 95 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 167 optimal weight:    5.9990
   chunk 177 optimal weight:    0.6980
   chunk 176 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.178232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.102688 restraints weight = 24570.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.105569 restraints weight = 11776.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.107150 restraints weight = 7776.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.107858 restraints weight = 6343.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.108475 restraints weight = 5797.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  14700  Z= 0.152
  Angle     :  0.681   9.807  20112  Z= 0.323
  Chirality :  0.042   0.186   2520
  Planarity :  0.005   0.077   2588
  Dihedral  :  4.345  53.818   2151
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.37 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 26.98 %
    Favored  : 67.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.20), residues: 1980
  helix:  1.57 (0.14), residues: 1306
  sheet: -0.51 (0.49), residues: 122
  loop : -2.43 (0.27), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  73 
 TYR   0.015   0.002   TYR D 102 
 PHE   0.022   0.001   PHE C  55 
 TRP   0.019   0.001   TRP B 375 
 HIS   0.006   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (14700)
  covalent geometry    : angle       0.68140 (20112)
  hydrogen bonds       : bond        0.04816 (  994)
  hydrogen bonds       : angle       4.13065 ( 2922)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 154
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   -4 TYR cc_start: 0.5566 (OUTLIER) cc_final: 0.4949 (t80)
REVERT: B  113 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8420 (mp)
REVERT: B  158 LEU cc_start: 0.9219 (tp) cc_final: 0.8982 (tt)
REVERT: B  170 MET cc_start: 0.8299 (ttp) cc_final: 0.7973 (ttm)
REVERT: B  372 ARG cc_start: 0.7089 (ttm-80) cc_final: 0.6797 (ptm160)
REVERT: B  376 MET cc_start: 0.8111 (tmm) cc_final: 0.7269 (tmm)
REVERT: B  460 HIS cc_start: 0.3959 (OUTLIER) cc_final: 0.2943 (m170)
REVERT: A   82 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8464 (tm-30)
REVERT: A  211 HIS cc_start: 0.7114 (OUTLIER) cc_final: 0.6689 (t-170)
REVERT: A  305 MET cc_start: 0.7974 (mmm) cc_final: 0.7625 (mmt)
REVERT: C  376 MET cc_start: 0.7965 (tmm) cc_final: 0.7746 (tmm)
REVERT: C  485 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6451 (mmp)
REVERT: D   88 ASP cc_start: 0.9129 (OUTLIER) cc_final: 0.8473 (t70)
REVERT: D  182 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7484 (tp)
REVERT: D  220 ARG cc_start: 0.8837 (mmt180) cc_final: 0.8519 (mmt90)
REVERT: D  305 MET cc_start: 0.8128 (mmp) cc_final: 0.7846 (mmt)
REVERT: D  353 MET cc_start: 0.8006 (mmm) cc_final: 0.7691 (mmm)
REVERT: D  355 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6983 (ppp)
REVERT: D  359 ASP cc_start: 0.8726 (t70) cc_final: 0.8269 (m-30)
REVERT: D  380 HIS cc_start: 0.7101 (t70) cc_final: 0.6748 (t70)
REVERT: D  437 GLN cc_start: 0.8503 (mt0) cc_final: 0.8032 (pt0)
  outliers start: 74
  outliers final: 44
  residues processed: 215
  average time/residue: 0.1093
  time to fit residues: 35.4743
Evaluate side-chains
  200 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 147
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   -4 TYR
Chi-restraints excluded: chain B residue    1 VAL
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  369 TRP
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  460 HIS
Chi-restraints excluded: chain A residue   82 GLN
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  211 HIS
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  228 PHE
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  375 PHE
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  390 ASN
Chi-restraints excluded: chain C residue  422 THR
Chi-restraints excluded: chain C residue  439 LEU
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain C residue  485 MET
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   71 LEU
Chi-restraints excluded: chain D residue   88 ASP
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   92 ARG
Chi-restraints excluded: chain D residue   96 ASN
Chi-restraints excluded: chain D residue   99 THR
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  228 PHE
Chi-restraints excluded: chain D residue  329 VAL
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain D residue  504 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 101 optimal weight:    0.5980
   chunk 3 optimal weight:    4.9990
   chunk 100 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 82 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 50 optimal weight:   20.0000
   chunk 37 optimal weight:   10.0000
   chunk 126 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 177 optimal weight:    0.7980
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
B   0 ASN
B  56 GLN
** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  56 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.177696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.101883 restraints weight = 24609.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.104718 restraints weight = 11869.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.106377 restraints weight = 7855.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.107220 restraints weight = 6374.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.107570 restraints weight = 5803.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.2860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  14700  Z= 0.152
  Angle     :  0.682  13.356  20112  Z= 0.322
  Chirality :  0.041   0.152   2520
  Planarity :  0.005   0.079   2588
  Dihedral  :  4.323  56.742   2151
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.47 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 27.94 %
    Favored  : 66.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.20), residues: 1980
  helix:  1.51 (0.15), residues: 1322
  sheet: -0.64 (0.49), residues: 122
  loop : -2.43 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  86 
 TYR   0.018   0.002   TYR C 108 
 PHE   0.020   0.001   PHE C 409 
 TRP   0.021   0.001   TRP B 375 
 HIS   0.006   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (14700)
  covalent geometry    : angle       0.68190 (20112)
  hydrogen bonds       : bond        0.04781 (  994)
  hydrogen bonds       : angle       4.07481 ( 2922)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 153
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   -4 TYR cc_start: 0.5503 (OUTLIER) cc_final: 0.4918 (t80)
REVERT: B  113 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8429 (mp)
REVERT: B  133 TYR cc_start: 0.8211 (m-80) cc_final: 0.6956 (m-80)
REVERT: B  158 LEU cc_start: 0.9236 (tp) cc_final: 0.8990 (tt)
REVERT: B  372 ARG cc_start: 0.7133 (ttm-80) cc_final: 0.6866 (ptm160)
REVERT: B  376 MET cc_start: 0.8106 (tmm) cc_final: 0.7262 (tmm)
REVERT: B  460 HIS cc_start: 0.3999 (OUTLIER) cc_final: 0.2812 (m170)
REVERT: A   82 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8440 (tm-30)
REVERT: A  211 HIS cc_start: 0.7128 (OUTLIER) cc_final: 0.6683 (t-170)
REVERT: C  376 MET cc_start: 0.7896 (tmm) cc_final: 0.7651 (tmm)
REVERT: C  485 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6253 (mmp)
REVERT: D   88 ASP cc_start: 0.9119 (OUTLIER) cc_final: 0.8442 (t70)
REVERT: D   92 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8182 (ttm170)
REVERT: D  182 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7535 (tp)
REVERT: D  220 ARG cc_start: 0.8875 (mmt180) cc_final: 0.8553 (mmt90)
REVERT: D  230 ARG cc_start: 0.8391 (mtm110) cc_final: 0.8036 (ttp-110)
REVERT: D  305 MET cc_start: 0.8096 (mmp) cc_final: 0.7810 (mmt)
REVERT: D  355 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.7075 (ppp)
REVERT: D  359 ASP cc_start: 0.8757 (t70) cc_final: 0.8305 (m-30)
REVERT: D  380 HIS cc_start: 0.7095 (t70) cc_final: 0.6734 (t70)
REVERT: D  439 ARG cc_start: 0.8467 (tpp80) cc_final: 0.8257 (tpp80)
  outliers start: 76
  outliers final: 56
  residues processed: 215
  average time/residue: 0.1139
  time to fit residues: 36.8771
Evaluate side-chains
  211 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 145
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   -4 TYR
Chi-restraints excluded: chain B residue    1 VAL
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  369 TRP
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  460 HIS
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   82 GLN
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  211 HIS
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  228 PHE
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  375 PHE
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  286 GLU
Chi-restraints excluded: chain C residue  320 MET
Chi-restraints excluded: chain C residue  373 LEU
Chi-restraints excluded: chain C residue  390 ASN
Chi-restraints excluded: chain C residue  422 THR
Chi-restraints excluded: chain C residue  439 LEU
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain C residue  485 MET
Chi-restraints excluded: chain C residue  492 VAL
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   71 LEU
Chi-restraints excluded: chain D residue   88 ASP
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   92 ARG
Chi-restraints excluded: chain D residue   96 ASN
Chi-restraints excluded: chain D residue   99 THR
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  228 PHE
Chi-restraints excluded: chain D residue  266 ILE
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain D residue  504 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 160 optimal weight:    0.7980
   chunk 136 optimal weight:    9.9990
   chunk 46 optimal weight:    5.9990
   chunk 179 optimal weight:    0.6980
   chunk 167 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 132 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 19 optimal weight:   30.0000
   chunk 191 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  56 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.177920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.104899 restraints weight = 24536.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.106857 restraints weight = 13700.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.106993 restraints weight = 8561.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.107620 restraints weight = 8045.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.107686 restraints weight = 7471.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.3066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  14700  Z= 0.144
  Angle     :  0.687  13.470  20112  Z= 0.322
  Chirality :  0.042   0.276   2520
  Planarity :  0.005   0.080   2588
  Dihedral  :  4.295  58.298   2151
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.22 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 28.21 %
    Favored  : 66.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.20), residues: 1980
  helix:  1.58 (0.14), residues: 1310
  sheet: -0.59 (0.50), residues: 122
  loop : -2.41 (0.27), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 438 
 TYR   0.018   0.002   TYR C 108 
 PHE   0.019   0.001   PHE D  24 
 TRP   0.024   0.001   TRP B 375 
 HIS   0.006   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (14700)
  covalent geometry    : angle       0.68713 (20112)
  hydrogen bonds       : bond        0.04657 (  994)
  hydrogen bonds       : angle       4.04091 ( 2922)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 156
  time to evaluate  : 0.513 
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: B   -4 TYR cc_start: 0.5257 (OUTLIER) cc_final: 0.4784 (t80)
REVERT: B  133 TYR cc_start: 0.8193 (m-80) cc_final: 0.6821 (m-80)
REVERT: B  158 LEU cc_start: 0.9269 (tp) cc_final: 0.9033 (tt)
REVERT: B  372 ARG cc_start: 0.7241 (ttm-80) cc_final: 0.6942 (ptm160)
REVERT: B  376 MET cc_start: 0.7998 (tmm) cc_final: 0.7129 (tmm)
REVERT: B  460 HIS cc_start: 0.4162 (OUTLIER) cc_final: 0.3147 (m170)
REVERT: A   82 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8429 (tm-30)
REVERT: A  211 HIS cc_start: 0.7145 (OUTLIER) cc_final: 0.6715 (t-170)
REVERT: A  305 MET cc_start: 0.7908 (mmm) cc_final: 0.7555 (mmt)
REVERT: A  426 LEU cc_start: 0.7564 (tt) cc_final: 0.7133 (pp)
REVERT: C   70 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6580 (tp30)
REVERT: C  376 MET cc_start: 0.7819 (tmm) cc_final: 0.7604 (tmm)
REVERT: C  485 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6333 (mmp)
REVERT: D   81 CYS cc_start: 0.8419 (t) cc_final: 0.8191 (m)
REVERT: D   88 ASP cc_start: 0.9121 (OUTLIER) cc_final: 0.8459 (t70)
REVERT: D  182 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7521 (tp)
REVERT: D  220 ARG cc_start: 0.9040 (mmt180) cc_final: 0.8643 (mmt90)
REVERT: D  222 ASP cc_start: 0.7821 (m-30) cc_final: 0.6384 (t0)
REVERT: D  230 ARG cc_start: 0.8512 (mtm110) cc_final: 0.8212 (ttp-110)
REVERT: D  355 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.7053 (ppp)
REVERT: D  359 ASP cc_start: 0.8781 (t70) cc_final: 0.8323 (m-30)
REVERT: D  362 ASN cc_start: 0.8464 (m-40) cc_final: 0.7653 (t0)
REVERT: D  380 HIS cc_start: 0.7068 (t70) cc_final: 0.6688 (t70)
REVERT: D  439 ARG cc_start: 0.8494 (tpp80) cc_final: 0.8288 (tpp80)
  outliers start: 74
  outliers final: 55
  residues processed: 219
  average time/residue: 0.1088
  time to fit residues: 35.5711
Evaluate side-chains
  212 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 149
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   -4 TYR
Chi-restraints excluded: chain B residue    1 VAL
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  136 GLN
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  460 HIS
Chi-restraints excluded: chain A residue   82 GLN
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  211 HIS
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  228 PHE
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  375 PHE
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  286 GLU
Chi-restraints excluded: chain C residue  320 MET
Chi-restraints excluded: chain C residue  373 LEU
Chi-restraints excluded: chain C residue  422 THR
Chi-restraints excluded: chain C residue  439 LEU
Chi-restraints excluded: chain C residue  485 MET
Chi-restraints excluded: chain C residue  492 VAL
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   71 LEU
Chi-restraints excluded: chain D residue   88 ASP
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   96 ASN
Chi-restraints excluded: chain D residue   99 THR
Chi-restraints excluded: chain D residue  173 VAL
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  228 PHE
Chi-restraints excluded: chain D residue  266 ILE
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain D residue  504 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 195 optimal weight:    0.0970
   chunk 78 optimal weight:    0.0470
   chunk 177 optimal weight:    1.9990
   chunk 156 optimal weight:    0.9980
   chunk 185 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   chunk 187 optimal weight:    4.9990
   chunk 179 optimal weight:    1.9990
   chunk 50 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9990
   chunk 197 optimal weight:    1.9990
   overall best weight:    0.8280

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 494 HIS
C  56 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.179569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.105268 restraints weight = 23803.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.107993 restraints weight = 11895.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.109605 restraints weight = 8000.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.110328 restraints weight = 6546.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.110726 restraints weight = 5970.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  14700  Z= 0.132
  Angle     :  0.691  12.981  20112  Z= 0.319
  Chirality :  0.041   0.143   2520
  Planarity :  0.005   0.077   2588
  Dihedral  :  4.243  59.620   2151
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.27 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 28.83 %
    Favored  : 66.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.20), residues: 1980
  helix:  1.59 (0.15), residues: 1316
  sheet: -0.52 (0.50), residues: 122
  loop : -2.32 (0.27), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 216 
 TYR   0.019   0.002   TYR C 108 
 PHE   0.031   0.001   PHE C 409 
 TRP   0.027   0.001   TRP B 375 
 HIS   0.007   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (14700)
  covalent geometry    : angle       0.69072 (20112)
  hydrogen bonds       : bond        0.04437 (  994)
  hydrogen bonds       : angle       3.97942 ( 2922)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 164
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   -4 TYR cc_start: 0.5393 (OUTLIER) cc_final: 0.4798 (t80)
REVERT: B  158 LEU cc_start: 0.9224 (tp) cc_final: 0.8997 (tt)
REVERT: B  170 MET cc_start: 0.8260 (ttp) cc_final: 0.8047 (ttm)
REVERT: B  372 ARG cc_start: 0.7208 (ttm-80) cc_final: 0.6856 (ptm160)
REVERT: B  376 MET cc_start: 0.8185 (tmm) cc_final: 0.7299 (tmm)
REVERT: B  460 HIS cc_start: 0.3989 (OUTLIER) cc_final: 0.2773 (m170)
REVERT: A   82 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8447 (tm-30)
REVERT: A  211 HIS cc_start: 0.7024 (OUTLIER) cc_final: 0.6587 (t-170)
REVERT: A  305 MET cc_start: 0.7976 (mmm) cc_final: 0.7642 (mmt)
REVERT: A  375 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7286 (m-80)
REVERT: A  426 LEU cc_start: 0.7597 (tt) cc_final: 0.7180 (pp)
REVERT: C   70 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6637 (tp30)
REVERT: C  485 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6398 (mmp)
REVERT: D   88 ASP cc_start: 0.9136 (OUTLIER) cc_final: 0.8581 (t0)
REVERT: D  182 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7531 (tp)
REVERT: D  220 ARG cc_start: 0.8850 (mmt180) cc_final: 0.8534 (mmt90)
REVERT: D  222 ASP cc_start: 0.7740 (m-30) cc_final: 0.6340 (t0)
REVERT: D  230 ARG cc_start: 0.8273 (mtm110) cc_final: 0.8005 (ttp-110)
REVERT: D  355 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.7125 (ppp)
REVERT: D  359 ASP cc_start: 0.8744 (t70) cc_final: 0.8319 (m-30)
REVERT: D  362 ASN cc_start: 0.8389 (m-40) cc_final: 0.7625 (t0)
REVERT: D  380 HIS cc_start: 0.7078 (t70) cc_final: 0.6702 (t70)
REVERT: D  437 GLN cc_start: 0.8482 (mt0) cc_final: 0.7886 (pt0)
REVERT: D  439 ARG cc_start: 0.8547 (tpp80) cc_final: 0.8305 (tpp80)
  outliers start: 72
  outliers final: 50
  residues processed: 227
  average time/residue: 0.1066
  time to fit residues: 36.3573
Evaluate side-chains
  211 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 152
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   -4 TYR
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  136 GLN
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  460 HIS
Chi-restraints excluded: chain A residue   82 GLN
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  211 HIS
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  228 PHE
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  375 PHE
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  507 THR
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  286 GLU
Chi-restraints excluded: chain C residue  320 MET
Chi-restraints excluded: chain C residue  373 LEU
Chi-restraints excluded: chain C residue  422 THR
Chi-restraints excluded: chain C residue  439 LEU
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain C residue  485 MET
Chi-restraints excluded: chain C residue  492 VAL
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   71 LEU
Chi-restraints excluded: chain D residue   88 ASP
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   96 ASN
Chi-restraints excluded: chain D residue   99 THR
Chi-restraints excluded: chain D residue  149 LEU
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  228 PHE
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain D residue  504 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 73 optimal weight:    5.9990
   chunk 131 optimal weight:   10.0000
   chunk 107 optimal weight:    9.9990
   chunk 113 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0020
   chunk 134 optimal weight:    0.9980
   chunk 40 optimal weight:    6.9990
   chunk 143 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 158 optimal weight:    1.9990
   overall best weight:    1.5592

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.177922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.108053 restraints weight = 24642.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.107329 restraints weight = 14901.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.106599 restraints weight = 10910.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.107206 restraints weight = 9489.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.107353 restraints weight = 8625.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.3392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  14700  Z= 0.155
  Angle     :  0.712  12.083  20112  Z= 0.333
  Chirality :  0.042   0.344   2520
  Planarity :  0.005   0.081   2588
  Dihedral  :  4.298  57.784   2151
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.97 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 28.21 %
    Favored  : 66.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.20), residues: 1980
  helix:  1.51 (0.15), residues: 1318
  sheet: -0.56 (0.50), residues: 122
  loop : -2.28 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 388 
 TYR   0.019   0.002   TYR C 108 
 PHE   0.021   0.001   PHE D  24 
 TRP   0.034   0.001   TRP C 369 
 HIS   0.007   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (14700)
  covalent geometry    : angle       0.71245 (20112)
  hydrogen bonds       : bond        0.04635 (  994)
  hydrogen bonds       : angle       4.00960 ( 2922)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 154
  time to evaluate  : 0.554 
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: B   -4 TYR cc_start: 0.5360 (OUTLIER) cc_final: 0.4726 (t80)
REVERT: B  133 TYR cc_start: 0.8245 (m-80) cc_final: 0.6826 (m-80)
REVERT: B  158 LEU cc_start: 0.9293 (tp) cc_final: 0.9050 (tt)
REVERT: B  372 ARG cc_start: 0.7253 (ttm-80) cc_final: 0.6986 (ptm160)
REVERT: B  376 MET cc_start: 0.8084 (tmm) cc_final: 0.7200 (tmm)
REVERT: B  460 HIS cc_start: 0.4186 (OUTLIER) cc_final: 0.3036 (m170)
REVERT: B  485 MET cc_start: 0.6498 (pmm) cc_final: 0.6284 (pmm)
REVERT: A   82 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8461 (tm-30)
REVERT: A  211 HIS cc_start: 0.7175 (OUTLIER) cc_final: 0.6725 (t-170)
REVERT: A  229 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7956 (tm-30)
REVERT: A  375 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7282 (m-80)
REVERT: A  381 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8789 (tt)
REVERT: C   70 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6536 (tp30)
REVERT: C  435 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.7010 (tp40)
REVERT: C  485 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6629 (mmp)
REVERT: D   88 ASP cc_start: 0.9133 (OUTLIER) cc_final: 0.8479 (t70)
REVERT: D  118 SER cc_start: 0.7613 (p) cc_final: 0.7331 (p)
REVERT: D  182 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7548 (tp)
REVERT: D  220 ARG cc_start: 0.9014 (mmt180) cc_final: 0.8598 (mmt90)
REVERT: D  221 LEU cc_start: 0.8823 (mt) cc_final: 0.8210 (mp)
REVERT: D  222 ASP cc_start: 0.7835 (m-30) cc_final: 0.6376 (t0)
REVERT: D  230 ARG cc_start: 0.8389 (mtm110) cc_final: 0.8134 (ttp-110)
REVERT: D  359 ASP cc_start: 0.8766 (t70) cc_final: 0.8353 (m-30)
REVERT: D  362 ASN cc_start: 0.8455 (m-40) cc_final: 0.7738 (t0)
REVERT: D  380 HIS cc_start: 0.7110 (t70) cc_final: 0.6746 (t70)
REVERT: D  437 GLN cc_start: 0.8404 (mt0) cc_final: 0.7836 (pt0)
  outliers start: 77
  outliers final: 57
  residues processed: 221
  average time/residue: 0.1050
  time to fit residues: 35.7066
Evaluate side-chains
  218 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 151
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   -4 TYR
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  136 GLN
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  460 HIS
Chi-restraints excluded: chain A residue   82 GLN
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  211 HIS
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  228 PHE
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  375 PHE
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  507 THR
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  286 GLU
Chi-restraints excluded: chain C residue  320 MET
Chi-restraints excluded: chain C residue  422 THR
Chi-restraints excluded: chain C residue  435 GLN
Chi-restraints excluded: chain C residue  439 LEU
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain C residue  485 MET
Chi-restraints excluded: chain C residue  492 VAL
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   71 LEU
Chi-restraints excluded: chain D residue   88 ASP
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   96 ASN
Chi-restraints excluded: chain D residue   99 THR
Chi-restraints excluded: chain D residue  149 LEU
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  228 PHE
Chi-restraints excluded: chain D residue  266 ILE
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  504 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 84 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 98 optimal weight:    4.9990
   chunk 96 optimal weight:    9.9990
   chunk 39 optimal weight:    4.9990
   chunk 190 optimal weight:    2.9990
   chunk 154 optimal weight:    4.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.176535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.100422 restraints weight = 24667.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.103189 restraints weight = 12077.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.104856 restraints weight = 8054.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.105609 restraints weight = 6565.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.105932 restraints weight = 5998.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.3520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  14700  Z= 0.176
  Angle     :  0.740  12.003  20112  Z= 0.344
  Chirality :  0.043   0.173   2520
  Planarity :  0.006   0.084   2588
  Dihedral  :  4.347  54.652   2151
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.37 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 28.55 %
    Favored  : 66.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.20), residues: 1980
  helix:  1.42 (0.14), residues: 1324
  sheet: -0.62 (0.49), residues: 124
  loop : -2.23 (0.28), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 388 
 TYR   0.020   0.002   TYR C 108 
 PHE   0.028   0.002   PHE C 409 
 TRP   0.049   0.002   TRP C 370 
 HIS   0.007   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 (14700)
  covalent geometry    : angle       0.74048 (20112)
  hydrogen bonds       : bond        0.04850 (  994)
  hydrogen bonds       : angle       4.06188 ( 2922)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 157
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   -4 TYR cc_start: 0.5601 (OUTLIER) cc_final: 0.4848 (t80)
REVERT: B   39 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8654 (mp)
REVERT: B  100 ARG cc_start: 0.7698 (mmt180) cc_final: 0.7393 (mmt180)
REVERT: B  133 TYR cc_start: 0.8394 (m-80) cc_final: 0.7030 (m-80)
REVERT: B  158 LEU cc_start: 0.9253 (tp) cc_final: 0.9008 (tt)
REVERT: B  376 MET cc_start: 0.8228 (tmm) cc_final: 0.7333 (tmm)
REVERT: B  460 HIS cc_start: 0.4149 (OUTLIER) cc_final: 0.2858 (m170)
REVERT: A   82 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8441 (tm-30)
REVERT: A  229 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7929 (tm-30)
REVERT: A  305 MET cc_start: 0.7849 (mmm) cc_final: 0.7446 (mmt)
REVERT: A  381 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8800 (tt)
REVERT: A  426 LEU cc_start: 0.7624 (tt) cc_final: 0.7099 (pp)
REVERT: A  499 PHE cc_start: 0.5529 (OUTLIER) cc_final: 0.4824 (t80)
REVERT: C   70 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6589 (tp30)
REVERT: C  320 MET cc_start: 0.3745 (OUTLIER) cc_final: 0.3006 (ttt)
REVERT: C  373 LEU cc_start: 0.8450 (tp) cc_final: 0.7821 (mt)
REVERT: C  376 MET cc_start: 0.8048 (tmm) cc_final: 0.7550 (tmm)
REVERT: C  435 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.6987 (tp40)
REVERT: C  485 MET cc_start: 0.6973 (OUTLIER) cc_final: 0.6544 (mmp)
REVERT: D   88 ASP cc_start: 0.9099 (OUTLIER) cc_final: 0.8437 (t70)
REVERT: D  118 SER cc_start: 0.7660 (p) cc_final: 0.7393 (p)
REVERT: D  182 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7616 (tp)
REVERT: D  220 ARG cc_start: 0.8907 (mmt180) cc_final: 0.8481 (mmt90)
REVERT: D  222 ASP cc_start: 0.7776 (m-30) cc_final: 0.6401 (t0)
REVERT: D  230 ARG cc_start: 0.8293 (mtm110) cc_final: 0.7963 (ttp-110)
REVERT: D  359 ASP cc_start: 0.8858 (t70) cc_final: 0.8381 (m-30)
REVERT: D  362 ASN cc_start: 0.8510 (m-40) cc_final: 0.7747 (t0)
REVERT: D  380 HIS cc_start: 0.7129 (t70) cc_final: 0.6758 (t70)
REVERT: D  439 ARG cc_start: 0.8544 (tpp80) cc_final: 0.8296 (tpp80)
  outliers start: 74
  outliers final: 52
  residues processed: 222
  average time/residue: 0.0935
  time to fit residues: 31.5717
Evaluate side-chains
  216 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 153
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   -4 TYR
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  136 GLN
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  460 HIS
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   82 GLN
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  211 HIS
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  228 PHE
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  375 PHE
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  499 PHE
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  507 THR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  286 GLU
Chi-restraints excluded: chain C residue  320 MET
Chi-restraints excluded: chain C residue  422 THR
Chi-restraints excluded: chain C residue  435 GLN
Chi-restraints excluded: chain C residue  439 LEU
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain C residue  485 MET
Chi-restraints excluded: chain C residue  492 VAL
Chi-restraints excluded: chain D residue   71 LEU
Chi-restraints excluded: chain D residue   88 ASP
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   96 ASN
Chi-restraints excluded: chain D residue   99 THR
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  228 PHE
Chi-restraints excluded: chain D residue  266 ILE
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  504 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 163 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 151 optimal weight:    0.9980
   chunk 190 optimal weight:    7.9990
   chunk 181 optimal weight:    2.9990
   chunk 108 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 174 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 129 optimal weight:    7.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 378 HIS
B 437 GLN
** A 211 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 = 0.4498 r_free = 0.4498 target = 0.178164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.102939 restraints weight = 24413.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.105805 restraints weight = 11744.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.107466 restraints weight = 7734.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.108274 restraints weight = 6287.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.108551 restraints weight = 5729.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.3649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  14700  Z= 0.137
  Angle     :  0.719  12.161  20112  Z= 0.331
  Chirality :  0.042   0.352   2520
  Planarity :  0.005   0.081   2588
  Dihedral  :  4.272  53.666   2151
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.42 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 29.10 %
    Favored  : 66.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.20), residues: 1980
  helix:  1.48 (0.14), residues: 1318
  sheet: -0.61 (0.49), residues: 124
  loop : -2.29 (0.27), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 388 
 TYR   0.019   0.001   TYR C 108 
 PHE   0.019   0.001   PHE D  24 
 TRP   0.050   0.002   TRP C 370 
 HIS   0.007   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (14700)
  covalent geometry    : angle       0.71941 (20112)
  hydrogen bonds       : bond        0.04517 (  994)
  hydrogen bonds       : angle       3.99345 ( 2922)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 153
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   -4 TYR cc_start: 0.5486 (OUTLIER) cc_final: 0.4966 (t80)
REVERT: B  100 ARG cc_start: 0.7694 (mmt180) cc_final: 0.7431 (mmt180)
REVERT: B  158 LEU cc_start: 0.9270 (tp) cc_final: 0.9035 (tt)
REVERT: B  376 MET cc_start: 0.8213 (tmm) cc_final: 0.7296 (tmm)
REVERT: B  460 HIS cc_start: 0.4043 (OUTLIER) cc_final: 0.2758 (m170)
REVERT: A   82 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8447 (tm-30)
REVERT: A  229 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7911 (tm-30)
REVERT: A  305 MET cc_start: 0.7887 (mmm) cc_final: 0.7491 (mmt)
REVERT: A  355 MET cc_start: 0.8071 (ptp) cc_final: 0.7771 (ptp)
REVERT: A  381 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8747 (tt)
REVERT: A  426 LEU cc_start: 0.7688 (tt) cc_final: 0.7218 (pp)
REVERT: A  499 PHE cc_start: 0.5542 (OUTLIER) cc_final: 0.4830 (t80)
REVERT: C   70 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6603 (tp30)
REVERT: C  157 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8232 (mt)
REVERT: C  320 MET cc_start: 0.3652 (OUTLIER) cc_final: 0.3360 (tpp)
REVERT: C  373 LEU cc_start: 0.8450 (tp) cc_final: 0.7917 (mt)
REVERT: C  435 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6986 (tp40)
REVERT: C  485 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6516 (mmp)
REVERT: D   88 ASP cc_start: 0.9124 (OUTLIER) cc_final: 0.8445 (t70)
REVERT: D  118 SER cc_start: 0.7664 (p) cc_final: 0.7141 (t)
REVERT: D  182 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7537 (tp)
REVERT: D  206 MET cc_start: 0.8802 (mmm) cc_final: 0.8415 (mmm)
REVERT: D  220 ARG cc_start: 0.8905 (mmt180) cc_final: 0.8490 (mmt90)
REVERT: D  222 ASP cc_start: 0.7754 (m-30) cc_final: 0.6389 (t0)
REVERT: D  230 ARG cc_start: 0.8254 (mtm110) cc_final: 0.7919 (ttp-110)
REVERT: D  355 MET cc_start: 0.7506 (mpp) cc_final: 0.7260 (ppp)
REVERT: D  359 ASP cc_start: 0.8838 (t70) cc_final: 0.8386 (m-30)
REVERT: D  362 ASN cc_start: 0.8552 (m-40) cc_final: 0.7877 (t0)
REVERT: D  380 HIS cc_start: 0.7015 (t70) cc_final: 0.6653 (t70)
REVERT: D  437 GLN cc_start: 0.8446 (mt0) cc_final: 0.7905 (pt0)
REVERT: D  439 ARG cc_start: 0.8559 (tpp80) cc_final: 0.8309 (tpp80)
  outliers start: 65
  outliers final: 50
  residues processed: 211
  average time/residue: 0.0890
  time to fit residues: 29.2092
Evaluate side-chains
  208 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 147
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   -4 TYR
Chi-restraints excluded: chain B residue    1 VAL
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  136 GLN
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  460 HIS
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   82 GLN
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  211 HIS
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  228 PHE
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  375 PHE
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  499 PHE
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  507 THR
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  286 GLU
Chi-restraints excluded: chain C residue  296 HIS
Chi-restraints excluded: chain C residue  320 MET
Chi-restraints excluded: chain C residue  422 THR
Chi-restraints excluded: chain C residue  435 GLN
Chi-restraints excluded: chain C residue  439 LEU
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain C residue  485 MET
Chi-restraints excluded: chain D residue   12 LEU
Chi-restraints excluded: chain D residue   71 LEU
Chi-restraints excluded: chain D residue   88 ASP
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   96 ASN
Chi-restraints excluded: chain D residue   99 THR
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  228 PHE
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  504 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 59 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 148 optimal weight:    0.5980
   chunk 133 optimal weight:    9.9990
   chunk 176 optimal weight:    0.8980
   chunk 76 optimal weight:    0.0870
   chunk 16 optimal weight:    7.9990
   chunk 4 optimal weight:    0.5980
   chunk 72 optimal weight:    8.9990
   chunk 122 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.6360

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

Flipped N/Q/H residues before XYZ refinement:
B 378 HIS
B 437 GLN
** A 211 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 = 0.4514 r_free = 0.4514 target = 0.179442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.106487 restraints weight = 24333.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.109027 restraints weight = 13500.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.109233 restraints weight = 7956.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.109653 restraints weight = 7213.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.109774 restraints weight = 7061.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.3804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  14700  Z= 0.131
  Angle     :  0.712  12.001  20112  Z= 0.327
  Chirality :  0.042   0.290   2520
  Planarity :  0.005   0.079   2588
  Dihedral  :  4.206  52.121   2151
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.07 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 29.64 %
    Favored  : 66.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.20), residues: 1980
  helix:  1.65 (0.14), residues: 1294
  sheet: -0.48 (0.52), residues: 114
  loop : -2.17 (0.27), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 388 
 TYR   0.019   0.001   TYR C 108 
 PHE   0.029   0.001   PHE C 409 
 TRP   0.047   0.002   TRP C 370 
 HIS   0.008   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (14700)
  covalent geometry    : angle       0.71236 (20112)
  hydrogen bonds       : bond        0.04265 (  994)
  hydrogen bonds       : angle       3.94215 ( 2922)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2861.52 seconds
wall clock time: 49 minutes 49.22 seconds (2989.22 seconds total)