Starting phenix.real_space_refine
on Wed Mar  4 09:38:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6j0m_9764/03_2026/6j0m_9764.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6j0m_9764/03_2026/6j0m_9764.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6j0m_9764/03_2026/6j0m_9764.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6j0m_9764/03_2026/6j0m_9764.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6j0m_9764/03_2026/6j0m_9764.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6j0m_9764/03_2026/6j0m_9764.map"
  }
  resolution = 3.9
  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=   0.001 sd=   0.013
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      42      5.16       5
     C    7974      2.51       5
     N    2208      2.21       5
     O    2361      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 129 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12585
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4195
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 535, 4195
          Classifications: {'peptide': 535}
          Link IDs: {'PTRANS': 21, 'TRANS': 513}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 2.74, per 1000 atoms: 0.22
  Number of scatterers: 12585
  At special positions: 0
  Unit cell: (95.285, 96.406, 143.488, 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      42     16.00
     O    2361      8.00
     N    2208      7.00
     C    7974      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: 0.85
  Conformation dependent library (CDL) restraints added in 585.4 milliseconds
  

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2994

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 30 sheets defined
      12.7% alpha, 34.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 50 through 60
      removed outlier: 3.680A  pdb=" N   GLU A  56 " --> pdb=" O   ASP A  52 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   HIS A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 109
    Processing helix  chain 'A' and resid 122 through 132
      removed outlier: 3.581A  pdb=" N   THR A 129 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 172
      removed outlier: 3.741A  pdb=" N   LEU A 165 " --> pdb=" O   TRP A 161 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   CYS A 166 " --> pdb=" O   HIS A 162 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ALA A 170 " --> pdb=" O   CYS A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 191
      removed outlier: 3.544A  pdb=" N   LYS A 191 " --> pdb=" O   ASP A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 294
      removed outlier: 3.594A  pdb=" N   GLN A 285 " --> pdb=" O   GLY A 281 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASN A 290 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   SER A 294 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 429
      No H-bonds generated for 'chain 'A' and resid 427 through 429'
    Processing helix  chain 'B' and resid 50 through 60
      removed outlier: 3.681A  pdb=" N   GLU B  56 " --> pdb=" O   ASP B  52 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   HIS B  59 " --> pdb=" O   THR B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 109
    Processing helix  chain 'B' and resid 122 through 132
      removed outlier: 3.582A  pdb=" N   THR B 129 " --> pdb=" O   ALA B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 172
      removed outlier: 3.742A  pdb=" N   LEU B 165 " --> pdb=" O   TRP B 161 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   CYS B 166 " --> pdb=" O   HIS B 162 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ALA B 170 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 191
      removed outlier: 3.543A  pdb=" N   LYS B 191 " --> pdb=" O   ASP B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 294
      removed outlier: 3.594A  pdb=" N   GLN B 285 " --> pdb=" O   GLY B 281 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN B 290 " --> pdb=" O   GLY B 286 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   SER B 294 " --> pdb=" O   ASN B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 427 through 429
      No H-bonds generated for 'chain 'B' and resid 427 through 429'
    Processing helix  chain 'C' and resid 50 through 60
      removed outlier: 3.680A  pdb=" N   GLU C  56 " --> pdb=" O   ASP C  52 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   HIS C  59 " --> pdb=" O   THR C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 109
    Processing helix  chain 'C' and resid 122 through 132
      removed outlier: 3.582A  pdb=" N   THR C 129 " --> pdb=" O   ALA C 125 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 172
      removed outlier: 3.741A  pdb=" N   LEU C 165 " --> pdb=" O   TRP C 161 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   CYS C 166 " --> pdb=" O   HIS C 162 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ALA C 170 " --> pdb=" O   CYS C 166 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 187 through 191
      removed outlier: 3.544A  pdb=" N   LYS C 191 " --> pdb=" O   ASP C 188 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 276 through 294
      removed outlier: 3.594A  pdb=" N   GLN C 285 " --> pdb=" O   GLY C 281 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN C 290 " --> pdb=" O   GLY C 286 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   SER C 294 " --> pdb=" O   ASN C 290 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 427 through 429
      No H-bonds generated for 'chain 'C' and resid 427 through 429'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14
      removed outlier: 4.747A  pdb=" N   ILE A   7 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   PHE A  80 " --> pdb=" O   LEU A  68 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   LEU A  70 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
      removed outlier: 4.938A  pdb=" N   VAL A  78 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   ILE A  84 " --> pdb=" O   LYS A 103 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   LYS A 103 " --> pdb=" O   ILE A  84 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   SER A  39 " --> pdb=" O   ALA A  19 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   ALA A  19 " --> pdb=" O   SER A  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96
      removed outlier: 4.751A  pdb=" N   ASP C 212 " --> pdb=" O   LEU C 301 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   LEU C 301 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLY C 325 " --> pdb=" O   LEU C 316 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   TYR C 196 " --> pdb=" O   GLN C 315 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   THR C 317 " --> pdb=" O   TYR C 196 " (cutoff:3.500A)
      removed outlier: 6.051A  pdb=" N   LEU C 198 " --> pdb=" O   THR C 317 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 116 through 118
    Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 139
      removed outlier: 3.608A  pdb=" N   VAL A 185 " --> pdb=" O   TRP A 174 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 195 through 199
      removed outlier: 6.476A  pdb=" N   TYR A 196 " --> pdb=" O   GLN A 315 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   THR A 317 " --> pdb=" O   TYR A 196 " (cutoff:3.500A)
      removed outlier: 6.051A  pdb=" N   LEU A 198 " --> pdb=" O   THR A 317 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLY A 325 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LEU A 301 " --> pdb=" O   ASP A 212 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   ASP A 212 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 14
      removed outlier: 4.747A  pdb=" N   ILE B   7 " --> pdb=" O   LEU B  14 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   PHE B  80 " --> pdb=" O   LEU B  68 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   LEU B  70 " --> pdb=" O   VAL B  78 " (cutoff:3.500A)
      removed outlier: 4.937A  pdb=" N   VAL B  78 " --> pdb=" O   LEU B  70 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   ILE B  84 " --> pdb=" O   LYS B 103 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   LYS B 103 " --> pdb=" O   ILE B  84 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   SER B  39 " --> pdb=" O   ALA B  19 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   ALA B  19 " --> pdb=" O   SER B  39 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 237 through 243
      removed outlier: 3.819A  pdb=" N   GLN A 237 " --> pdb=" O   ASP A 232 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   GLY A 230 " --> pdb=" O   GLN A 239 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLY A 241 " --> pdb=" O   VAL A 228 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   VAL A 228 " --> pdb=" O   GLY A 241 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   ARG A 243 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
      removed outlier: 5.184A  pdb=" N   LEU A 226 " --> pdb=" O   ARG A 243 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLU A 227 " --> pdb=" O   TRP A 267 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 365 through 369
      removed outlier: 7.587A  pdb=" N   TRP A 397 " --> pdb=" O   PRO A 433 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   ILE A 435 " --> pdb=" O   TRP A 397 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   ARG A 399 " --> pdb=" O   ILE A 435 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   GLY A 437 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ILE A 422 " --> pdb=" O   LEU A 436 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   ALA A 438 " --> pdb=" O   GLU A 420 " (cutoff:3.500A)
      removed outlier: 7.349A  pdb=" N   GLU A 420 " --> pdb=" O   ALA A 438 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ALA A 367 " --> pdb=" O   VAL A 421 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 411 through 412
    Processing sheet with id=AB1, first strand: chain 'A' and resid 488 through 491
    Processing sheet with id=AB2, first strand: chain 'A' and resid 461 through 462
    Processing sheet with id=AB3, first strand: chain 'A' and resid 503 through 508
      removed outlier: 6.174A  pdb=" N   LEU A 504 " --> pdb=" O   ASN C 512 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   THR C 514 " --> pdb=" O   LEU A 504 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   LEU A 506 " --> pdb=" O   THR C 514 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'A' and resid 510 through 515
    Processing sheet with id=AB5, first strand: chain 'A' and resid 519 through 522
      removed outlier: 3.510A  pdb=" N   ILE C 529 " --> pdb=" O   ASN B 535 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 519 through 522
      removed outlier: 5.632A  pdb=" N   GLU A 528 " --> pdb=" O   MET B 521 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   VAL A 527 " --> pdb=" O   ASN C 535 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   THR C 537 " --> pdb=" O   VAL A 527 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   ILE A 529 " --> pdb=" O   THR C 537 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'A' and resid 534 through 537
      removed outlier: 3.516A  pdb=" N   ASN A 535 " --> pdb=" O   VAL B 527 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE B 529 " --> pdb=" O   ASN A 535 " (cutoff:3.500A)
      removed outlier: 5.616A  pdb=" N   GLU B 528 " --> pdb=" O   MET C 521 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 116 through 118
    Processing sheet with id=AB9, first strand: chain 'B' and resid 138 through 139
      removed outlier: 3.608A  pdb=" N   VAL B 185 " --> pdb=" O   TRP B 174 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 195 through 199
      removed outlier: 6.476A  pdb=" N   TYR B 196 " --> pdb=" O   GLN B 315 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   THR B 317 " --> pdb=" O   TYR B 196 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   LEU B 198 " --> pdb=" O   THR B 317 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLY B 325 " --> pdb=" O   LEU B 316 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LEU B 301 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   ASP B 212 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 12 through 14
      removed outlier: 4.746A  pdb=" N   ILE C   7 " --> pdb=" O   LEU C  14 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   PHE C  80 " --> pdb=" O   LEU C  68 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   LEU C  70 " --> pdb=" O   VAL C  78 " (cutoff:3.500A)
      removed outlier: 4.937A  pdb=" N   VAL C  78 " --> pdb=" O   LEU C  70 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   ILE C  84 " --> pdb=" O   LYS C 103 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   LYS C 103 " --> pdb=" O   ILE C  84 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   SER C  39 " --> pdb=" O   ALA C  19 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   ALA C  19 " --> pdb=" O   SER C  39 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 237 through 243
      removed outlier: 3.819A  pdb=" N   GLN B 237 " --> pdb=" O   ASP B 232 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLY B 230 " --> pdb=" O   GLN B 239 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLY B 241 " --> pdb=" O   VAL B 228 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   VAL B 228 " --> pdb=" O   GLY B 241 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   ARG B 243 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
      removed outlier: 5.183A  pdb=" N   LEU B 226 " --> pdb=" O   ARG B 243 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLU B 227 " --> pdb=" O   TRP B 267 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 365 through 369
      removed outlier: 7.587A  pdb=" N   TRP B 397 " --> pdb=" O   PRO B 433 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   ILE B 435 " --> pdb=" O   TRP B 397 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   ARG B 399 " --> pdb=" O   ILE B 435 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   GLY B 437 " --> pdb=" O   ARG B 399 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ILE B 422 " --> pdb=" O   LEU B 436 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   ALA B 438 " --> pdb=" O   GLU B 420 " (cutoff:3.500A)
      removed outlier: 7.349A  pdb=" N   GLU B 420 " --> pdb=" O   ALA B 438 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ALA B 367 " --> pdb=" O   VAL B 421 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 411 through 412
    Processing sheet with id=AC6, first strand: chain 'B' and resid 461 through 462
    Processing sheet with id=AC7, first strand: chain 'B' and resid 510 through 515
    Processing sheet with id=AC8, first strand: chain 'C' and resid 116 through 118
    Processing sheet with id=AC9, first strand: chain 'C' and resid 138 through 139
      removed outlier: 3.607A  pdb=" N   VAL C 185 " --> pdb=" O   TRP C 174 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'C' and resid 237 through 243
      removed outlier: 3.818A  pdb=" N   GLN C 237 " --> pdb=" O   ASP C 232 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLY C 230 " --> pdb=" O   GLN C 239 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLY C 241 " --> pdb=" O   VAL C 228 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   VAL C 228 " --> pdb=" O   GLY C 241 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   ARG C 243 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
      removed outlier: 5.183A  pdb=" N   LEU C 226 " --> pdb=" O   ARG C 243 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLU C 227 " --> pdb=" O   TRP C 267 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'C' and resid 365 through 369
      removed outlier: 7.587A  pdb=" N   TRP C 397 " --> pdb=" O   PRO C 433 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   ILE C 435 " --> pdb=" O   TRP C 397 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   ARG C 399 " --> pdb=" O   ILE C 435 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   GLY C 437 " --> pdb=" O   ARG C 399 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ILE C 422 " --> pdb=" O   LEU C 436 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   ALA C 438 " --> pdb=" O   GLU C 420 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   GLU C 420 " --> pdb=" O   ALA C 438 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ALA C 367 " --> pdb=" O   VAL C 421 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'C' and resid 461 through 462

    391 hydrogen bonds defined for protein.
    1020 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: 2.02

  Time building geometry restraints manager: 1.19 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4146
        1.34 -     1.46: 2122
        1.46 -     1.57: 6473
        1.57 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 12807
  Sorted by residual:
  bond pdb=" CA  TRP A 267 "
       pdb=" CB  TRP A 267 "
    ideal  model  delta    sigma   weight residual
    1.534  1.504  0.030 1.78e-02 3.16e+03 2.82e+00
  bond pdb=" CA  TRP B 267 "
       pdb=" CB  TRP B 267 "
    ideal  model  delta    sigma   weight residual
    1.534  1.504  0.029 1.78e-02 3.16e+03 2.72e+00
  bond pdb=" C   ASN A 222 "
       pdb=" N   PRO A 223 "
    ideal  model  delta    sigma   weight residual
    1.333  1.313  0.019 1.17e-02 7.31e+03 2.70e+00
  bond pdb=" C   ASN C 222 "
       pdb=" N   PRO C 223 "
    ideal  model  delta    sigma   weight residual
    1.333  1.314  0.019 1.17e-02 7.31e+03 2.68e+00
  bond pdb=" CA  TRP C 267 "
       pdb=" CB  TRP C 267 "
    ideal  model  delta    sigma   weight residual
    1.534  1.505  0.029 1.78e-02 3.16e+03 2.66e+00
  ... (remaining 12802 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 16400
        1.98 -     3.96: 798
        3.96 -     5.94: 85
        5.94 -     7.92: 28
        7.92 -     9.90: 5
  Bond angle restraints: 17316
  Sorted by residual:
  angle pdb=" N   GLY B 484 "
        pdb=" CA  GLY B 484 "
        pdb=" C   GLY B 484 "
      ideal   model   delta    sigma   weight residual
     112.68  107.56    5.12 1.26e+00 6.30e-01 1.65e+01
  angle pdb=" N   GLY A 484 "
        pdb=" CA  GLY A 484 "
        pdb=" C   GLY A 484 "
      ideal   model   delta    sigma   weight residual
     112.68  107.57    5.11 1.26e+00 6.30e-01 1.64e+01
  angle pdb=" N   GLY C 484 "
        pdb=" CA  GLY C 484 "
        pdb=" C   GLY C 484 "
      ideal   model   delta    sigma   weight residual
     112.68  107.61    5.07 1.26e+00 6.30e-01 1.62e+01
  angle pdb=" CA  LYS A 235 "
        pdb=" CB  LYS A 235 "
        pdb=" CG  LYS A 235 "
      ideal   model   delta    sigma   weight residual
     114.10  121.64   -7.54 2.00e+00 2.50e-01 1.42e+01
  angle pdb=" CA  LYS C 235 "
        pdb=" CB  LYS C 235 "
        pdb=" CG  LYS C 235 "
      ideal   model   delta    sigma   weight residual
     114.10  121.64   -7.54 2.00e+00 2.50e-01 1.42e+01
  ... (remaining 17311 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 6825
       17.97 -    35.94: 806
       35.94 -    53.91: 151
       53.91 -    71.89: 21
       71.89 -    89.86: 15
  Dihedral angle restraints: 7818
    sinusoidal: 3189
      harmonic: 4629
  Sorted by residual:
  dihedral pdb=" CA  GLY B 304 "
           pdb=" C   GLY B 304 "
           pdb=" N   ASP B 305 "
           pdb=" CA  ASP B 305 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.82  -35.18     0      5.00e+00 4.00e-02 4.95e+01
  dihedral pdb=" CA  GLY A 304 "
           pdb=" C   GLY A 304 "
           pdb=" N   ASP A 305 "
           pdb=" CA  ASP A 305 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.82  -35.18     0      5.00e+00 4.00e-02 4.95e+01
  dihedral pdb=" CA  GLY C 304 "
           pdb=" C   GLY C 304 "
           pdb=" N   ASP C 305 "
           pdb=" CA  ASP C 305 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.88  -35.12     0      5.00e+00 4.00e-02 4.93e+01
  ... (remaining 7815 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1485
       0.059 -    0.117: 410
       0.117 -    0.176: 70
       0.176 -    0.235: 7
       0.235 -    0.293: 5
  Chirality restraints: 1977
  Sorted by residual:
  chirality pdb=" CB  ILE A  91 "
            pdb=" CA  ILE A  91 "
            pdb=" CG1 ILE A  91 "
            pdb=" CG2 ILE A  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.29 2.00e-01 2.50e+01 2.15e+00
  chirality pdb=" CB  ILE C  91 "
            pdb=" CA  ILE C  91 "
            pdb=" CG1 ILE C  91 "
            pdb=" CG2 ILE C  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.29 2.00e-01 2.50e+01 2.11e+00
  chirality pdb=" CB  ILE B  91 "
            pdb=" CA  ILE B  91 "
            pdb=" CG1 ILE B  91 "
            pdb=" CG2 ILE B  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.29 2.00e-01 2.50e+01 2.09e+00
  ... (remaining 1974 not shown)

  Planarity restraints: 2226
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 355 "   -0.045 5.00e-02 4.00e+02   6.57e-02 6.90e+00
        pdb=" N   PRO B 356 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO B 356 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 356 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 355 "    0.044 5.00e-02 4.00e+02   6.55e-02 6.86e+00
        pdb=" N   PRO C 356 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO C 356 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO C 356 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 355 "   -0.044 5.00e-02 4.00e+02   6.54e-02 6.85e+00
        pdb=" N   PRO A 356 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 356 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 356 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 2223 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 3407
        2.81 -     3.33: 10628
        3.33 -     3.85: 20037
        3.85 -     4.38: 23042
        4.38 -     4.90: 41234
  Nonbonded interactions: 98348
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 124 "
            pdb=" OG  SER A 128 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" O   LYS B 124 "
            pdb=" OG  SER B 128 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" O   LYS C 124 "
            pdb=" OG  SER C 128 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OG  SER B 255 "
            pdb=" O   ASP B 257 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" OG  SER C 255 "
            pdb=" O   ASP C 257 "
     model   vdw
     2.342 3.040
  ... (remaining 98343 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  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:             1.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.810
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
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      :  0.007   0.047  12807  Z= 0.336
  Angle     :  0.980   9.902  17316  Z= 0.561
  Chirality :  0.056   0.293   1977
  Planarity :  0.007   0.066   2226
  Dihedral  : 15.907  89.858   4824
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 12.44 %
    Favored  : 86.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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: -4.05 (0.17), residues: 1593
  helix: -4.47 (0.15), residues: 159
  sheet: -2.50 (0.19), residues: 525
  loop : -2.47 (0.16), residues: 909

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 167 
 TYR   0.017   0.002   TYR B 354 
 PHE   0.023   0.002   PHE C 411 
 TRP   0.020   0.003   TRP B 267 
 HIS   0.005   0.001   HIS A 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00733 (12807)
  covalent geometry    : angle       0.98049 (17316)
  hydrogen bonds       : bond        0.27938 (  391)
  hydrogen bonds       : angle      11.42940 ( 1020)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 281
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 ASP cc_start: 0.5730 (p0) cc_final: 0.5490 (p0)
REVERT: A  257 ASP cc_start: 0.8330 (m-30) cc_final: 0.8018 (m-30)
REVERT: A  312 ASP cc_start: 0.8275 (p0) cc_final: 0.7893 (p0)
REVERT: A  374 GLN cc_start: 0.7371 (tm-30) cc_final: 0.7102 (tm-30)
REVERT: A  494 LYS cc_start: 0.7602 (pttp) cc_final: 0.7291 (ptmt)
REVERT: B  218 ASP cc_start: 0.7240 (m-30) cc_final: 0.7021 (m-30)
REVERT: B  257 ASP cc_start: 0.8486 (m-30) cc_final: 0.8270 (m-30)
REVERT: B  269 ILE cc_start: 0.9036 (pt) cc_final: 0.8803 (mp)
REVERT: B  494 LYS cc_start: 0.7472 (pttp) cc_final: 0.7200 (ptmt)
REVERT: C   26 TYR cc_start: 0.8949 (m-80) cc_final: 0.8612 (m-80)
REVERT: C  120 ASP cc_start: 0.6304 (p0) cc_final: 0.6087 (p0)
REVERT: C  257 ASP cc_start: 0.8297 (m-30) cc_final: 0.8048 (m-30)
REVERT: C  494 LYS cc_start: 0.7258 (pttp) cc_final: 0.6950 (ptmt)
REVERT: C  521 MET cc_start: 0.6498 (ttm) cc_final: 0.6076 (tpp)
  outliers start: 12
  outliers final: 3
  residues processed: 287
  average time/residue: 0.1231
  time to fit residues: 49.2758
Evaluate side-chains
  175 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 172
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain C residue  461 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    7.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:   20.0000
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0170
   chunk 149 optimal weight:    4.9990
   overall best weight:    2.8024

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

Flipped N/Q/H residues before XYZ refinement:
A   4 GLN
A 152 GLN
A 222 ASN
A 322 GLN
A 373 GLN
A 428 ASN
** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 441 ASN
A 482 ASN
** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 509 GLN
B 152 GLN
B 222 ASN
B 236 GLN
B 322 GLN
B 428 ASN
** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 482 ASN
** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 GLN
C 152 GLN
C 222 ASN
C 428 ASN
C 441 ASN
C 482 ASN
** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 509 GLN

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.113243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.104637 restraints weight = 20414.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.105496 restraints weight = 17490.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.106144 restraints weight = 15231.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.106614 restraints weight = 12860.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.106680 restraints weight = 11502.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12807  Z= 0.158
  Angle     :  0.642   9.279  17316  Z= 0.335
  Chirality :  0.046   0.150   1977
  Planarity :  0.004   0.041   2226
  Dihedral  :  6.246  28.041   1707
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 16.99 %
    Favored  : 80.04 %
  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: -2.98 (0.19), residues: 1593
  helix: -2.19 (0.34), residues: 168
  sheet: -1.96 (0.20), residues: 561
  loop : -1.90 (0.19), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  86 
 TYR   0.014   0.001   TYR A 354 
 PHE   0.011   0.001   PHE B 411 
 TRP   0.012   0.002   TRP B 267 
 HIS   0.003   0.001   HIS A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (12807)
  covalent geometry    : angle       0.64233 (17316)
  hydrogen bonds       : bond        0.03672 (  391)
  hydrogen bonds       : angle       7.41641 ( 1020)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 219
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  257 ASP cc_start: 0.7999 (m-30) cc_final: 0.7771 (m-30)
REVERT: B  358 LEU cc_start: 0.6463 (tt) cc_final: 0.5991 (tp)
REVERT: B  534 ILE cc_start: 0.6594 (OUTLIER) cc_final: 0.6300 (tp)
REVERT: C   26 TYR cc_start: 0.8979 (m-80) cc_final: 0.8632 (m-80)
REVERT: C  120 ASP cc_start: 0.5685 (p0) cc_final: 0.5458 (p0)
REVERT: C  290 ASN cc_start: 0.7760 (m-40) cc_final: 0.7558 (m110)
REVERT: C  358 LEU cc_start: 0.5961 (tt) cc_final: 0.5513 (tp)
  outliers start: 41
  outliers final: 27
  residues processed: 244
  average time/residue: 0.1045
  time to fit residues: 37.6777
Evaluate side-chains
  180 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 152
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  215 TRP
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  308 TYR
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain C residue   91 ILE
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  174 TRP
Chi-restraints excluded: chain C residue  215 TRP
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  460 ILE
Chi-restraints excluded: chain C residue  461 VAL
Chi-restraints excluded: chain C residue  490 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 156 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   chunk 37 optimal weight:   10.0000
   chunk 74 optimal weight:    0.4980
   chunk 56 optimal weight:    6.9990
   chunk 113 optimal weight:    8.9990
   chunk 151 optimal weight:    5.9990
   chunk 49 optimal weight:    4.9990
   chunk 52 optimal weight:   20.0000
   overall best weight:    3.6988

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

Flipped N/Q/H residues before XYZ refinement:
A 220 GLN
A 322 GLN
** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 236 GLN
B 322 GLN
** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.110233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.098799 restraints weight = 21442.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.100526 restraints weight = 14952.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.101794 restraints weight = 11435.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.102705 restraints weight = 9276.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.103422 restraints weight = 7839.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12807  Z= 0.183
  Angle     :  0.635   7.656  17316  Z= 0.327
  Chirality :  0.046   0.154   1977
  Planarity :  0.004   0.041   2226
  Dihedral  :  5.968  32.477   1707
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 17.72 %
    Favored  : 77.22 %
  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: -2.72 (0.19), residues: 1593
  helix: -1.76 (0.37), residues: 183
  sheet: -1.66 (0.22), residues: 537
  loop : -1.88 (0.18), residues: 873

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 381 
 TYR   0.012   0.001   TYR A 354 
 PHE   0.012   0.002   PHE A 411 
 TRP   0.014   0.002   TRP B 267 
 HIS   0.003   0.001   HIS A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (12807)
  covalent geometry    : angle       0.63451 (17316)
  hydrogen bonds       : bond        0.03509 (  391)
  hydrogen bonds       : angle       6.90623 ( 1020)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 180
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
REVERT: A  315 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8075 (pt0)
REVERT: A  373 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7712 (mp10)
REVERT: A  534 ILE cc_start: 0.6192 (OUTLIER) cc_final: 0.5690 (tp)
REVERT: B  315 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8156 (pt0)
REVERT: B  358 LEU cc_start: 0.6643 (tt) cc_final: 0.6256 (tp)
REVERT: B  534 ILE cc_start: 0.6836 (OUTLIER) cc_final: 0.6425 (tp)
REVERT: C   26 TYR cc_start: 0.8928 (m-80) cc_final: 0.8558 (m-80)
REVERT: C  534 ILE cc_start: 0.5877 (OUTLIER) cc_final: 0.5430 (tp)
  outliers start: 70
  outliers final: 45
  residues processed: 235
  average time/residue: 0.0932
  time to fit residues: 33.4464
Evaluate side-chains
  208 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 157
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  315 GLN
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  373 GLN
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  215 TRP
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  308 TYR
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue   62 VAL
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  174 TRP
Chi-restraints excluded: chain C residue  215 TRP
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain C residue  324 ASP
Chi-restraints excluded: chain C residue  329 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  346 VAL
Chi-restraints excluded: chain C residue  461 VAL
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  534 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 19 optimal weight:   20.0000
   chunk 139 optimal weight:    9.9990
   chunk 94 optimal weight:    4.9990
   chunk 95 optimal weight:    0.7980
   chunk 34 optimal weight:    9.9990
   chunk 37 optimal weight:    8.9990
   chunk 130 optimal weight:   10.0000
   chunk 82 optimal weight:    7.9990
   chunk 120 optimal weight:   10.0000
   chunk 104 optimal weight:   30.0000
   overall best weight:    6.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 GLN
** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  59 HIS
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 290 ASN
C 337 ASN
** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 491 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.106900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.095337 restraints weight = 21637.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.097055 restraints weight = 15278.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.098251 restraints weight = 11721.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.099046 restraints weight = 9578.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.099781 restraints weight = 8237.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053  12807  Z= 0.287
  Angle     :  0.723   9.443  17316  Z= 0.371
  Chirality :  0.049   0.167   1977
  Planarity :  0.004   0.040   2226
  Dihedral  :  6.289  35.153   1707
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 21.33 %
    Favored  : 73.17 %
  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: -2.73 (0.20), residues: 1593
  helix: -1.49 (0.39), residues: 183
  sheet: -1.71 (0.22), residues: 537
  loop : -1.92 (0.19), residues: 873

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 381 
 TYR   0.013   0.002   TYR A 354 
 PHE   0.014   0.002   PHE B 163 
 TRP   0.019   0.002   TRP B 267 
 HIS   0.004   0.001   HIS C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00664 (12807)
  covalent geometry    : angle       0.72325 (17316)
  hydrogen bonds       : bond        0.03773 (  391)
  hydrogen bonds       : angle       7.11298 ( 1020)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 157
  time to evaluate  : 0.461 
Fit side-chains
REVERT: A  315 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8157 (pt0)
REVERT: A  373 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7682 (mp10)
REVERT: A  534 ILE cc_start: 0.6284 (OUTLIER) cc_final: 0.5801 (tp)
REVERT: B  214 TYR cc_start: 0.8719 (t80) cc_final: 0.8066 (t80)
REVERT: B  315 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8245 (pt0)
REVERT: B  515 MET cc_start: 0.7899 (mpp) cc_final: 0.7588 (mpp)
REVERT: B  534 ILE cc_start: 0.7156 (OUTLIER) cc_final: 0.6664 (tp)
REVERT: C   26 TYR cc_start: 0.8930 (m-80) cc_final: 0.8569 (m-80)
REVERT: C  153 MET cc_start: 0.8441 (tpt) cc_final: 0.7955 (tpt)
REVERT: C  227 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6902 (pt0)
REVERT: C  358 LEU cc_start: 0.6307 (tt) cc_final: 0.5929 (tp)
REVERT: C  534 ILE cc_start: 0.6726 (OUTLIER) cc_final: 0.6288 (tp)
  outliers start: 76
  outliers final: 55
  residues processed: 212
  average time/residue: 0.0925
  time to fit residues: 30.4611
Evaluate side-chains
  199 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 137
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  206 LYS
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  315 GLN
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  373 GLN
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  486 ASN
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  174 TRP
Chi-restraints excluded: chain B residue  206 LYS
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  215 TRP
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  308 TYR
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  486 ASN
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   94 LYS
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  174 TRP
Chi-restraints excluded: chain C residue  215 TRP
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain C residue  324 ASP
Chi-restraints excluded: chain C residue  329 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  346 VAL
Chi-restraints excluded: chain C residue  355 LEU
Chi-restraints excluded: chain C residue  460 ILE
Chi-restraints excluded: chain C residue  461 VAL
Chi-restraints excluded: chain C residue  504 LEU
Chi-restraints excluded: chain C residue  534 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 56 optimal weight:    3.9990
   chunk 120 optimal weight:    0.7980
   chunk 123 optimal weight:    5.9990
   chunk 121 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 35 optimal weight:    7.9990
   chunk 106 optimal weight:   20.0000
   chunk 16 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 77 optimal weight:    9.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 GLN
** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 440 HIS
B 150 HIS
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 337 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.109840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.098307 restraints weight = 21361.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.100065 restraints weight = 14999.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.101331 restraints weight = 11461.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.102238 restraints weight = 9308.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.102956 restraints weight = 7896.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.3007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12807  Z= 0.153
  Angle     :  0.617   8.721  17316  Z= 0.314
  Chirality :  0.045   0.155   1977
  Planarity :  0.003   0.037   2226
  Dihedral  :  5.869  34.021   1707
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 22.49 %
    Favored  : 72.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.45 (0.20), residues: 1593
  helix: -1.26 (0.39), residues: 183
  sheet: -1.37 (0.23), residues: 519
  loop : -1.87 (0.19), residues: 891

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 381 
 TYR   0.009   0.001   TYR A 354 
 PHE   0.014   0.001   PHE C 411 
 TRP   0.011   0.002   TRP C 215 
 HIS   0.004   0.001   HIS B 440 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (12807)
  covalent geometry    : angle       0.61731 (17316)
  hydrogen bonds       : bond        0.03088 (  391)
  hydrogen bonds       : angle       6.58451 ( 1020)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 172
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
REVERT: A  373 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7652 (mp10)
REVERT: A  534 ILE cc_start: 0.6161 (OUTLIER) cc_final: 0.5719 (tp)
REVERT: B  214 TYR cc_start: 0.8682 (t80) cc_final: 0.8036 (t80)
REVERT: B  315 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8168 (pt0)
REVERT: B  515 MET cc_start: 0.7799 (mpp) cc_final: 0.7530 (mpp)
REVERT: B  534 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6366 (tp)
REVERT: C   26 TYR cc_start: 0.8889 (m-80) cc_final: 0.8607 (m-80)
REVERT: C  534 ILE cc_start: 0.6299 (OUTLIER) cc_final: 0.5911 (tp)
  outliers start: 75
  outliers final: 54
  residues processed: 225
  average time/residue: 0.0937
  time to fit residues: 32.3506
Evaluate side-chains
  212 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 153
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  206 LYS
Chi-restraints excluded: chain A residue  215 TRP
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  373 GLN
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  486 ASN
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  123 GLU
Chi-restraints excluded: chain B residue  206 LYS
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  215 TRP
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  308 TYR
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  486 ASN
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  174 TRP
Chi-restraints excluded: chain C residue  215 TRP
Chi-restraints excluded: chain C residue  321 SER
Chi-restraints excluded: chain C residue  324 ASP
Chi-restraints excluded: chain C residue  329 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  346 VAL
Chi-restraints excluded: chain C residue  355 LEU
Chi-restraints excluded: chain C residue  386 LEU
Chi-restraints excluded: chain C residue  461 VAL
Chi-restraints excluded: chain C residue  486 ASN
Chi-restraints excluded: chain C residue  534 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 78 optimal weight:    0.0870
   chunk 76 optimal weight:    1.9990
   chunk 154 optimal weight:   10.0000
   chunk 39 optimal weight:    7.9990
   chunk 100 optimal weight:    7.9990
   chunk 158 optimal weight:    5.9990
   chunk 95 optimal weight:    5.9990
   chunk 150 optimal weight:    3.9990
   chunk 57 optimal weight:    6.9990
   chunk 53 optimal weight:   20.0000
   overall best weight:    3.6166

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 337 ASN
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.109457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.097926 restraints weight = 21220.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.099652 restraints weight = 14925.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.100848 restraints weight = 11478.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.101756 restraints weight = 9397.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.102509 restraints weight = 7975.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.3173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12807  Z= 0.178
  Angle     :  0.633   8.712  17316  Z= 0.320
  Chirality :  0.045   0.159   1977
  Planarity :  0.003   0.035   2226
  Dihedral  :  5.779  34.478   1707
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 23.28 %
    Favored  : 70.86 %
  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: -2.37 (0.20), residues: 1593
  helix: -1.07 (0.39), residues: 183
  sheet: -1.32 (0.23), residues: 537
  loop : -1.84 (0.19), residues: 873

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 431 
 TYR   0.010   0.001   TYR A 354 
 PHE   0.013   0.002   PHE A 411 
 TRP   0.012   0.002   TRP B 267 
 HIS   0.003   0.001   HIS B 440 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 (12807)
  covalent geometry    : angle       0.63256 (17316)
  hydrogen bonds       : bond        0.03124 (  391)
  hydrogen bonds       : angle       6.50601 ( 1020)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 163
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8102 (tpt) cc_final: 0.7532 (tpp)
REVERT: A  315 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8140 (pt0)
REVERT: A  373 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7625 (mp10)
REVERT: A  534 ILE cc_start: 0.6186 (OUTLIER) cc_final: 0.5757 (tp)
REVERT: B  150 HIS cc_start: 0.7810 (OUTLIER) cc_final: 0.7489 (m90)
REVERT: B  214 TYR cc_start: 0.8669 (t80) cc_final: 0.7991 (t80)
REVERT: B  272 SER cc_start: 0.9083 (t) cc_final: 0.8551 (p)
REVERT: B  315 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8179 (pt0)
REVERT: B  515 MET cc_start: 0.7816 (mpp) cc_final: 0.7540 (mpp)
REVERT: B  534 ILE cc_start: 0.6875 (OUTLIER) cc_final: 0.6344 (tp)
REVERT: C   26 TYR cc_start: 0.8860 (m-80) cc_final: 0.8583 (m-80)
REVERT: C  153 MET cc_start: 0.8216 (tpt) cc_final: 0.7893 (tpt)
REVERT: C  308 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.8065 (m-80)
REVERT: C  534 ILE cc_start: 0.6470 (OUTLIER) cc_final: 0.6041 (tp)
  outliers start: 81
  outliers final: 69
  residues processed: 222
  average time/residue: 0.0872
  time to fit residues: 29.9339
Evaluate side-chains
  226 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 149
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  206 LYS
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  215 TRP
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  315 GLN
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  373 GLN
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  486 ASN
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  123 GLU
Chi-restraints excluded: chain B residue  150 HIS
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  174 TRP
Chi-restraints excluded: chain B residue  206 LYS
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  215 TRP
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  308 TYR
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  486 ASN
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   94 LYS
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  174 TRP
Chi-restraints excluded: chain C residue  215 TRP
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain C residue  308 TYR
Chi-restraints excluded: chain C residue  321 SER
Chi-restraints excluded: chain C residue  324 ASP
Chi-restraints excluded: chain C residue  329 ILE
Chi-restraints excluded: chain C residue  337 ASN
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  346 VAL
Chi-restraints excluded: chain C residue  355 LEU
Chi-restraints excluded: chain C residue  386 LEU
Chi-restraints excluded: chain C residue  461 VAL
Chi-restraints excluded: chain C residue  486 ASN
Chi-restraints excluded: chain C residue  504 LEU
Chi-restraints excluded: chain C residue  534 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 157 optimal weight:   20.0000
   chunk 155 optimal weight:    5.9990
   chunk 89 optimal weight:   10.0000
   chunk 45 optimal weight:   10.0000
   chunk 16 optimal weight:    4.9990
   chunk 100 optimal weight:   10.0000
   chunk 51 optimal weight:   10.0000
   chunk 61 optimal weight:   10.0000
   chunk 132 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 15 optimal weight:   10.0000
   overall best weight:    7.5992

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 337 ASN
** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 337 ASN
** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 334 HIS
** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.105179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.093698 restraints weight = 21612.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.095337 restraints weight = 15346.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.096459 restraints weight = 11893.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.097365 restraints weight = 9791.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.097971 restraints weight = 8385.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.3334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.062  12807  Z= 0.328
  Angle     :  0.764   9.891  17316  Z= 0.389
  Chirality :  0.050   0.177   1977
  Planarity :  0.004   0.040   2226
  Dihedral  :  6.379  39.146   1707
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  6.36 %
    Allowed  : 23.50 %
    Favored  : 70.14 %
  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: -2.70 (0.20), residues: 1593
  helix: -1.22 (0.39), residues: 183
  sheet: -1.74 (0.22), residues: 561
  loop : -1.92 (0.19), residues: 849

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 105 
 TYR   0.012   0.002   TYR A 354 
 PHE   0.015   0.002   PHE B 163 
 TRP   0.018   0.003   TRP C 267 
 HIS   0.005   0.001   HIS C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00761 (12807)
  covalent geometry    : angle       0.76426 (17316)
  hydrogen bonds       : bond        0.03829 (  391)
  hydrogen bonds       : angle       7.04286 ( 1020)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 155
  time to evaluate  : 0.540 
Fit side-chains
REVERT: A  153 MET cc_start: 0.8134 (tpt) cc_final: 0.7203 (tpp)
REVERT: A  315 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8225 (pt0)
REVERT: A  373 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7502 (mp10)
REVERT: A  534 ILE cc_start: 0.6326 (OUTLIER) cc_final: 0.5900 (tp)
REVERT: B  150 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7511 (m90)
REVERT: B  214 TYR cc_start: 0.8736 (t80) cc_final: 0.8048 (t80)
REVERT: B  218 ASP cc_start: 0.7525 (m-30) cc_final: 0.7259 (m-30)
REVERT: B  315 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8305 (pt0)
REVERT: B  336 LEU cc_start: 0.8872 (mm) cc_final: 0.8624 (mp)
REVERT: B  478 MET cc_start: 0.7029 (ttt) cc_final: 0.6770 (ttt)
REVERT: B  515 MET cc_start: 0.7950 (mpp) cc_final: 0.7670 (mpp)
REVERT: B  534 ILE cc_start: 0.7117 (OUTLIER) cc_final: 0.6625 (tp)
REVERT: C   26 TYR cc_start: 0.8920 (m-80) cc_final: 0.8648 (m-80)
REVERT: C  308 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.8008 (m-80)
REVERT: C  534 ILE cc_start: 0.7095 (OUTLIER) cc_final: 0.6638 (tp)
  outliers start: 88
  outliers final: 72
  residues processed: 221
  average time/residue: 0.0921
  time to fit residues: 31.6348
Evaluate side-chains
  227 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 147
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  206 LYS
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  215 TRP
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  315 GLN
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  337 ASN
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  373 GLN
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  486 ASN
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  150 HIS
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  174 TRP
Chi-restraints excluded: chain B residue  206 LYS
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  215 TRP
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  486 ASN
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   94 LYS
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  174 TRP
Chi-restraints excluded: chain C residue  215 TRP
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain C residue  308 TYR
Chi-restraints excluded: chain C residue  321 SER
Chi-restraints excluded: chain C residue  324 ASP
Chi-restraints excluded: chain C residue  329 ILE
Chi-restraints excluded: chain C residue  337 ASN
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  346 VAL
Chi-restraints excluded: chain C residue  355 LEU
Chi-restraints excluded: chain C residue  386 LEU
Chi-restraints excluded: chain C residue  461 VAL
Chi-restraints excluded: chain C residue  486 ASN
Chi-restraints excluded: chain C residue  504 LEU
Chi-restraints excluded: chain C residue  534 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 147 optimal weight:    0.8980
   chunk 55 optimal weight:    0.0870
   chunk 113 optimal weight:    9.9990
   chunk 97 optimal weight:    6.9990
   chunk 99 optimal weight:    9.9990
   chunk 16 optimal weight:    0.8980
   chunk 56 optimal weight:   10.0000
   chunk 138 optimal weight:    5.9990
   chunk 156 optimal weight:   20.0000
   chunk 81 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.3762

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

Flipped N/Q/H residues before XYZ refinement:
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 337 ASN
** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.112122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.100856 restraints weight = 20910.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.102628 restraints weight = 14688.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.103904 restraints weight = 11179.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.104820 restraints weight = 9040.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.105450 restraints weight = 7635.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.3482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12807  Z= 0.104
  Angle     :  0.598   8.536  17316  Z= 0.299
  Chirality :  0.044   0.146   1977
  Planarity :  0.003   0.032   2226
  Dihedral  :  5.597  35.575   1707
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 24.87 %
    Favored  : 70.35 %
  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: -2.30 (0.20), residues: 1593
  helix: -0.98 (0.38), residues: 183
  sheet: -1.30 (0.23), residues: 543
  loop : -1.79 (0.19), residues: 867

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 338 
 TYR   0.011   0.001   TYR C 372 
 PHE   0.017   0.001   PHE B 411 
 TRP   0.014   0.002   TRP C 342 
 HIS   0.004   0.001   HIS B 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (12807)
  covalent geometry    : angle       0.59801 (17316)
  hydrogen bonds       : bond        0.02761 (  391)
  hydrogen bonds       : angle       6.12039 ( 1020)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 188
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  301 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8459 (tt)
REVERT: A  315 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8130 (pt0)
REVERT: A  373 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7542 (mp10)
REVERT: A  534 ILE cc_start: 0.6042 (OUTLIER) cc_final: 0.5569 (tp)
REVERT: B  150 HIS cc_start: 0.7764 (OUTLIER) cc_final: 0.7471 (m90)
REVERT: B  214 TYR cc_start: 0.8663 (t80) cc_final: 0.7972 (t80)
REVERT: B  272 SER cc_start: 0.9018 (t) cc_final: 0.8498 (p)
REVERT: B  315 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8208 (pt0)
REVERT: B  515 MET cc_start: 0.7628 (mpp) cc_final: 0.7382 (mpp)
REVERT: B  534 ILE cc_start: 0.6838 (OUTLIER) cc_final: 0.6387 (tp)
REVERT: C   26 TYR cc_start: 0.8837 (m-80) cc_final: 0.8585 (m-80)
REVERT: C  259 LEU cc_start: 0.8371 (mp) cc_final: 0.8167 (mp)
REVERT: C  534 ILE cc_start: 0.6285 (OUTLIER) cc_final: 0.5845 (tp)
  outliers start: 66
  outliers final: 50
  residues processed: 235
  average time/residue: 0.0978
  time to fit residues: 34.5481
Evaluate side-chains
  224 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 166
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  206 LYS
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  215 TRP
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  315 GLN
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  373 GLN
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  486 ASN
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  123 GLU
Chi-restraints excluded: chain B residue  150 HIS
Chi-restraints excluded: chain B residue  206 LYS
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  215 TRP
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  486 ASN
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  174 TRP
Chi-restraints excluded: chain C residue  206 LYS
Chi-restraints excluded: chain C residue  215 TRP
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain C residue  321 SER
Chi-restraints excluded: chain C residue  324 ASP
Chi-restraints excluded: chain C residue  329 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  346 VAL
Chi-restraints excluded: chain C residue  355 LEU
Chi-restraints excluded: chain C residue  386 LEU
Chi-restraints excluded: chain C residue  461 VAL
Chi-restraints excluded: chain C residue  486 ASN
Chi-restraints excluded: chain C residue  534 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 136 optimal weight:   10.0000
   chunk 53 optimal weight:   20.0000
   chunk 58 optimal weight:    8.9990
   chunk 144 optimal weight:    0.7980
   chunk 101 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 102 optimal weight:    7.9990
   chunk 107 optimal weight:   10.0000
   chunk 98 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   chunk 120 optimal weight:    7.9990
   overall best weight:    3.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 150 HIS
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 GLN
** C 220 GLN ** 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 = 0.3248 r_free = 0.3248 target = 0.109740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.098335 restraints weight = 21029.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.100046 restraints weight = 14859.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.101245 restraints weight = 11426.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.102144 restraints weight = 9319.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.102900 restraints weight = 7915.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12807  Z= 0.172
  Angle     :  0.643   8.581  17316  Z= 0.319
  Chirality :  0.046   0.153   1977
  Planarity :  0.003   0.033   2226
  Dihedral  :  5.655  36.021   1707
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 25.38 %
    Favored  : 69.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.29 (0.20), residues: 1593
  helix: -0.81 (0.39), residues: 183
  sheet: -1.37 (0.22), residues: 555
  loop : -1.76 (0.20), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 399 
 TYR   0.009   0.001   TYR B 404 
 PHE   0.014   0.001   PHE B 411 
 TRP   0.012   0.002   TRP A 215 
 HIS   0.009   0.001   HIS C 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (12807)
  covalent geometry    : angle       0.64278 (17316)
  hydrogen bonds       : bond        0.03028 (  391)
  hydrogen bonds       : angle       6.26716 ( 1020)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 165
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8125 (tpt) cc_final: 0.7538 (tpp)
REVERT: A  315 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8128 (pt0)
REVERT: A  373 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7427 (mp10)
REVERT: A  534 ILE cc_start: 0.6156 (OUTLIER) cc_final: 0.5712 (tp)
REVERT: B  272 SER cc_start: 0.9060 (t) cc_final: 0.8553 (p)
REVERT: B  315 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8209 (pt0)
REVERT: B  534 ILE cc_start: 0.6937 (OUTLIER) cc_final: 0.6428 (tp)
REVERT: C   26 TYR cc_start: 0.8871 (m-80) cc_final: 0.8602 (m-80)
REVERT: C  534 ILE cc_start: 0.6419 (OUTLIER) cc_final: 0.5978 (tp)
  outliers start: 68
  outliers final: 56
  residues processed: 211
  average time/residue: 0.0923
  time to fit residues: 30.2194
Evaluate side-chains
  220 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 158
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  206 LYS
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  215 TRP
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  315 GLN
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  373 GLN
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  486 ASN
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  123 GLU
Chi-restraints excluded: chain B residue  174 TRP
Chi-restraints excluded: chain B residue  206 LYS
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  215 TRP
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  486 ASN
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  174 TRP
Chi-restraints excluded: chain C residue  206 LYS
Chi-restraints excluded: chain C residue  215 TRP
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain C residue  321 SER
Chi-restraints excluded: chain C residue  324 ASP
Chi-restraints excluded: chain C residue  329 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  346 VAL
Chi-restraints excluded: chain C residue  355 LEU
Chi-restraints excluded: chain C residue  386 LEU
Chi-restraints excluded: chain C residue  439 MET
Chi-restraints excluded: chain C residue  461 VAL
Chi-restraints excluded: chain C residue  486 ASN
Chi-restraints excluded: chain C residue  534 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 113 optimal weight:    6.9990
   chunk 97 optimal weight:    0.9990
   chunk 136 optimal weight:    9.9990
   chunk 138 optimal weight:   10.0000
   chunk 151 optimal weight:   10.0000
   chunk 107 optimal weight:    9.9990
   chunk 80 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 109 optimal weight:    3.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 150 HIS
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 452 GLN
C   3 HIS
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.110563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.099139 restraints weight = 21059.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.100879 restraints weight = 14767.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.102155 restraints weight = 11258.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.103132 restraints weight = 9089.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.103762 restraints weight = 7697.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.3616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12807  Z= 0.153
  Angle     :  0.632   8.357  17316  Z= 0.313
  Chirality :  0.045   0.163   1977
  Planarity :  0.003   0.032   2226
  Dihedral  :  5.564  35.926   1707
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 25.38 %
    Favored  : 69.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.21 (0.20), residues: 1593
  helix: -0.72 (0.38), residues: 183
  sheet: -1.20 (0.23), residues: 537
  loop : -1.81 (0.19), residues: 873

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 399 
 TYR   0.010   0.001   TYR A 372 
 PHE   0.015   0.001   PHE B 411 
 TRP   0.011   0.002   TRP C 342 
 HIS   0.008   0.001   HIS C 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (12807)
  covalent geometry    : angle       0.63202 (17316)
  hydrogen bonds       : bond        0.02926 (  391)
  hydrogen bonds       : angle       6.14295 ( 1020)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 171
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8109 (tpt) cc_final: 0.7556 (tpp)
REVERT: A  315 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8087 (pt0)
REVERT: A  373 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7622 (mp10)
REVERT: A  534 ILE cc_start: 0.6096 (OUTLIER) cc_final: 0.5677 (tp)
REVERT: B  150 HIS cc_start: 0.7759 (OUTLIER) cc_final: 0.7343 (m90)
REVERT: B  272 SER cc_start: 0.8953 (t) cc_final: 0.8391 (p)
REVERT: B  315 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8180 (pt0)
REVERT: B  511 MET cc_start: 0.7941 (tmm) cc_final: 0.7688 (tmm)
REVERT: B  515 MET cc_start: 0.7647 (mpp) cc_final: 0.7390 (mpp)
REVERT: B  534 ILE cc_start: 0.6853 (OUTLIER) cc_final: 0.6404 (tp)
REVERT: C    3 HIS cc_start: 0.7474 (OUTLIER) cc_final: 0.7227 (m90)
REVERT: C   26 TYR cc_start: 0.8870 (m-80) cc_final: 0.8613 (m-80)
REVERT: C  301 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8524 (tt)
REVERT: C  534 ILE cc_start: 0.6404 (OUTLIER) cc_final: 0.5961 (tp)
  outliers start: 67
  outliers final: 56
  residues processed: 216
  average time/residue: 0.0977
  time to fit residues: 32.4282
Evaluate side-chains
  230 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 165
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  206 LYS
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  215 TRP
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  315 GLN
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  373 GLN
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  486 ASN
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  150 HIS
Chi-restraints excluded: chain B residue  174 TRP
Chi-restraints excluded: chain B residue  206 LYS
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  215 TRP
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  337 ASN
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  486 ASN
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain C residue    3 HIS
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  174 TRP
Chi-restraints excluded: chain C residue  206 LYS
Chi-restraints excluded: chain C residue  215 TRP
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain C residue  321 SER
Chi-restraints excluded: chain C residue  324 ASP
Chi-restraints excluded: chain C residue  329 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  346 VAL
Chi-restraints excluded: chain C residue  355 LEU
Chi-restraints excluded: chain C residue  386 LEU
Chi-restraints excluded: chain C residue  439 MET
Chi-restraints excluded: chain C residue  461 VAL
Chi-restraints excluded: chain C residue  486 ASN
Chi-restraints excluded: chain C residue  534 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 109 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 32 optimal weight:    8.9990
   chunk 72 optimal weight:    6.9990
   chunk 20 optimal weight:    9.9990
   chunk 81 optimal weight:    9.9990
   chunk 77 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 452 GLN
C   3 HIS
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 491 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.109236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.097762 restraints weight = 21268.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.099491 restraints weight = 14941.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.100768 restraints weight = 11456.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.101724 restraints weight = 9278.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.102395 restraints weight = 7824.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.3638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12807  Z= 0.189
  Angle     :  0.659   8.744  17316  Z= 0.327
  Chirality :  0.046   0.164   1977
  Planarity :  0.003   0.033   2226
  Dihedral  :  5.653  36.911   1707
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 25.02 %
    Favored  : 69.85 %
  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: -2.21 (0.20), residues: 1593
  helix: -0.63 (0.39), residues: 183
  sheet: -1.22 (0.23), residues: 537
  loop : -1.81 (0.19), residues: 873

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 399 
 TYR   0.011   0.001   TYR B 404 
 PHE   0.013   0.002   PHE B 411 
 TRP   0.012   0.002   TRP A 215 
 HIS   0.004   0.001   HIS C 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (12807)
  covalent geometry    : angle       0.65861 (17316)
  hydrogen bonds       : bond        0.03104 (  391)
  hydrogen bonds       : angle       6.23021 ( 1020)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1589.51 seconds
wall clock time: 28 minutes 31.58 seconds (1711.58 seconds total)