Starting phenix.real_space_refine
on Mon Aug 25 19:39:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dli_46979/08_2025/9dli_46979.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dli_46979/08_2025/9dli_46979.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dli_46979/08_2025/9dli_46979.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dli_46979/08_2025/9dli_46979.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dli_46979/08_2025/9dli_46979.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dli_46979/08_2025/9dli_46979.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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: 5
    Type Number    sf(0)   Gaussians
     S      80      5.16       5
     C   10060      2.51       5
     N    2392      2.21       5
     O    2704      1.98       5
     H   15064      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 91 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 30300
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A1"
      Number of atoms: 7575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 462, 7575
          Classifications: {'peptide': 462}
          Link IDs: {'PTRANS': 10, 'TRANS': 451}
          Chain breaks: 2
    Chain: "A2"
      Number of atoms: 7575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 462, 7575
          Classifications: {'peptide': 462}
          Link IDs: {'PTRANS': 10, 'TRANS': 451}
          Chain breaks: 2
    Chain: "A3"
      Number of atoms: 7575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 462, 7575
          Classifications: {'peptide': 462}
          Link IDs: {'PTRANS': 10, 'TRANS': 451}
          Chain breaks: 2
    Chain: "A4"
      Number of atoms: 7575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 462, 7575
          Classifications: {'peptide': 462}
          Link IDs: {'PTRANS': 10, 'TRANS': 451}
          Chain breaks: 2
  Time building chain proxies: 4.30, per 1000 atoms: 0.14
  Number of scatterers: 30300
  At special positions: 0
  Unit cell: (113.548, 113.872, 100.932, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      80     16.00
     O    2704      8.00
     N    2392      7.00
     C   10060      6.00
     H   15064      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYSA1 152 " - pdb=" SG  CYSA1 165 " distance=2.03
    Simple disulfide: pdb=" SG  CYSA2 152 " - pdb=" SG  CYSA2 165 " distance=2.03
    Simple disulfide: pdb=" SG  CYSA3 152 " - pdb=" SG  CYSA3 165 " distance=2.03
    Simple disulfide: pdb=" SG  CYSA4 152 " - pdb=" SG  CYSA4 165 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.09
  Conformation dependent library (CDL) restraints added in 655.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3544

  Finding SS restraints...
    Secondary structure from input PDB file:
      73 helices and 12 sheets defined
      61.3% alpha, 11.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'A1' and resid 34 through 61
      removed outlier: 3.716A  pdb=" N   SERA1  40 " --> pdb=" O   LYSA1  36 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ARGA1  43 " --> pdb=" O   LYSA1  39 " (cutoff:3.500A)
    Processing helix  chain 'A1' and resid 62 through 64
      No H-bonds generated for 'chain 'A1' and resid 62 through 64'
    Processing helix  chain 'A1' and resid 65 through 79
      removed outlier: 3.909A  pdb=" N   TYRA1  69 " --> pdb=" O   SERA1  65 " (cutoff:3.500A)
    Processing helix  chain 'A1' and resid 90 through 94
    Processing helix  chain 'A1' and resid 96 through 106
    Processing helix  chain 'A1' and resid 106 through 113
    Processing helix  chain 'A1' and resid 155 through 159
      removed outlier: 3.711A  pdb=" N   ARGA1 159 " --> pdb=" O   GLNA1 156 " (cutoff:3.500A)
    Processing helix  chain 'A1' and resid 219 through 233
    Processing helix  chain 'A1' and resid 288 through 314
    Processing helix  chain 'A1' and resid 326 through 353
      removed outlier: 3.521A  pdb=" N   SERA1 351 " --> pdb=" O   ILEA1 347 " (cutoff:3.500A)
    Processing helix  chain 'A1' and resid 353 through 360
      removed outlier: 3.910A  pdb=" N   LEUA1 357 " --> pdb=" O   VALA1 353 " (cutoff:3.500A)
    Processing helix  chain 'A1' and resid 369 through 393
    Processing helix  chain 'A1' and resid 394 through 397
    Processing helix  chain 'A1' and resid 403 through 441
      removed outlier: 4.730A  pdb=" N   LYSA1 416 " --> pdb=" O   SERA1 412 " (cutoff:3.500A)
      removed outlier: 5.401A  pdb=" N   ASPA1 417 " --> pdb=" O   ARGA1 413 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ILEA1 428 " --> pdb=" O   META1 424 " (cutoff:3.500A)
    Processing helix  chain 'A1' and resid 444 through 448
    Processing helix  chain 'A1' and resid 449 through 463
    Processing helix  chain 'A1' and resid 466 through 474
      removed outlier: 3.649A  pdb=" N   ASNA1 474 " --> pdb=" O   ILEA1 470 " (cutoff:3.500A)
    Processing helix  chain 'A1' and resid 476 through 490
      removed outlier: 3.881A  pdb=" N   ILEA1 480 " --> pdb=" O   VALA1 476 " (cutoff:3.500A)
    Processing helix  chain 'A1' and resid 493 through 513
      removed outlier: 4.224A  pdb=" N   PHEA1 497 " --> pdb=" O   LEUA1 493 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   LEUA1 498 " --> pdb=" O   LEUA1 494 " (cutoff:3.500A)
    Processing helix  chain 'A2' and resid 35 through 62
      removed outlier: 3.878A  pdb=" N   SERA2  40 " --> pdb=" O   LYSA2  36 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ARGA2  43 " --> pdb=" O   LYSA2  39 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   META2  62 " --> pdb=" O   LEUA2  58 " (cutoff:3.500A)
    Processing helix  chain 'A2' and resid 65 through 79
      removed outlier: 3.876A  pdb=" N   TYRA2  69 " --> pdb=" O   SERA2  65 " (cutoff:3.500A)
    Processing helix  chain 'A2' and resid 90 through 94
    Processing helix  chain 'A2' and resid 96 through 106
    Processing helix  chain 'A2' and resid 106 through 113
    Processing helix  chain 'A2' and resid 219 through 233
    Processing helix  chain 'A2' and resid 288 through 314
      removed outlier: 3.903A  pdb=" N   CYSA2 302 " --> pdb=" O   GLUA2 298 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   PHEA2 303 " --> pdb=" O   ILEA2 299 " (cutoff:3.500A)
    Processing helix  chain 'A2' and resid 326 through 353
      removed outlier: 3.645A  pdb=" N   SERA2 351 " --> pdb=" O   ILEA2 347 " (cutoff:3.500A)
    Processing helix  chain 'A2' and resid 353 through 360
      removed outlier: 3.670A  pdb=" N   LEUA2 357 " --> pdb=" O   VALA2 353 " (cutoff:3.500A)
    Processing helix  chain 'A2' and resid 369 through 393
    Processing helix  chain 'A2' and resid 394 through 397
    Processing helix  chain 'A2' and resid 401 through 441
      removed outlier: 3.581A  pdb=" N   GLNA2 406 " --> pdb=" O   ARGA2 402 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   LYSA2 416 " --> pdb=" O   SERA2 412 " (cutoff:3.500A)
      removed outlier: 5.426A  pdb=" N   ASPA2 417 " --> pdb=" O   ARGA2 413 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ILEA2 428 " --> pdb=" O   META2 424 " (cutoff:3.500A)
    Processing helix  chain 'A2' and resid 444 through 448
    Processing helix  chain 'A2' and resid 449 through 463
    Processing helix  chain 'A2' and resid 466 through 474
      removed outlier: 3.568A  pdb=" N   ILEA2 470 " --> pdb=" O   ASNA2 466 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ASNA2 474 " --> pdb=" O   ILEA2 470 " (cutoff:3.500A)
    Processing helix  chain 'A2' and resid 476 through 490
      removed outlier: 3.781A  pdb=" N   ILEA2 480 " --> pdb=" O   VALA2 476 " (cutoff:3.500A)
    Processing helix  chain 'A2' and resid 493 through 513
      removed outlier: 4.264A  pdb=" N   PHEA2 497 " --> pdb=" O   LEUA2 493 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   LEUA2 498 " --> pdb=" O   LEUA2 494 " (cutoff:3.500A)
    Processing helix  chain 'A3' and resid 35 through 61
      removed outlier: 3.642A  pdb=" N   SERA3  40 " --> pdb=" O   LYSA3  36 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ARGA3  43 " --> pdb=" O   LYSA3  39 " (cutoff:3.500A)
    Processing helix  chain 'A3' and resid 62 through 64
      No H-bonds generated for 'chain 'A3' and resid 62 through 64'
    Processing helix  chain 'A3' and resid 65 through 79
      removed outlier: 4.035A  pdb=" N   TYRA3  69 " --> pdb=" O   SERA3  65 " (cutoff:3.500A)
    Processing helix  chain 'A3' and resid 90 through 94
      removed outlier: 3.522A  pdb=" N   LEUA3  94 " --> pdb=" O   PHEA3  91 " (cutoff:3.500A)
    Processing helix  chain 'A3' and resid 96 through 106
    Processing helix  chain 'A3' and resid 106 through 113
    Processing helix  chain 'A3' and resid 219 through 233
    Processing helix  chain 'A3' and resid 288 through 314
      removed outlier: 3.731A  pdb=" N   CYSA3 302 " --> pdb=" O   GLUA3 298 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   PHEA3 303 " --> pdb=" O   ILEA3 299 " (cutoff:3.500A)
    Processing helix  chain 'A3' and resid 326 through 353
      removed outlier: 3.648A  pdb=" N   THRA3 350 " --> pdb=" O   ASNA3 346 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   SERA3 351 " --> pdb=" O   ILEA3 347 " (cutoff:3.500A)
    Processing helix  chain 'A3' and resid 353 through 360
      removed outlier: 3.666A  pdb=" N   LEUA3 357 " --> pdb=" O   VALA3 353 " (cutoff:3.500A)
    Processing helix  chain 'A3' and resid 369 through 393
    Processing helix  chain 'A3' and resid 394 through 397
    Processing helix  chain 'A3' and resid 403 through 441
      removed outlier: 4.714A  pdb=" N   LYSA3 416 " --> pdb=" O   SERA3 412 " (cutoff:3.500A)
      removed outlier: 5.404A  pdb=" N   ASPA3 417 " --> pdb=" O   ARGA3 413 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ILEA3 428 " --> pdb=" O   META3 424 " (cutoff:3.500A)
    Processing helix  chain 'A3' and resid 444 through 448
    Processing helix  chain 'A3' and resid 449 through 463
    Processing helix  chain 'A3' and resid 466 through 474
      removed outlier: 3.537A  pdb=" N   ILEA3 470 " --> pdb=" O   ASNA3 466 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ASNA3 474 " --> pdb=" O   ILEA3 470 " (cutoff:3.500A)
    Processing helix  chain 'A3' and resid 476 through 491
      removed outlier: 3.862A  pdb=" N   ILEA3 480 " --> pdb=" O   VALA3 476 " (cutoff:3.500A)
    Processing helix  chain 'A3' and resid 493 through 513
      removed outlier: 4.274A  pdb=" N   PHEA3 497 " --> pdb=" O   LEUA3 493 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   LEUA3 498 " --> pdb=" O   LEUA3 494 " (cutoff:3.500A)
    Processing helix  chain 'A4' and resid 35 through 61
    Processing helix  chain 'A4' and resid 62 through 64
      No H-bonds generated for 'chain 'A4' and resid 62 through 64'
    Processing helix  chain 'A4' and resid 65 through 79
      removed outlier: 3.958A  pdb=" N   TYRA4  69 " --> pdb=" O   SERA4  65 " (cutoff:3.500A)
    Processing helix  chain 'A4' and resid 90 through 94
    Processing helix  chain 'A4' and resid 96 through 106
    Processing helix  chain 'A4' and resid 106 through 113
    Processing helix  chain 'A4' and resid 155 through 159
      removed outlier: 3.653A  pdb=" N   ARGA4 159 " --> pdb=" O   GLNA4 156 " (cutoff:3.500A)
    Processing helix  chain 'A4' and resid 219 through 233
    Processing helix  chain 'A4' and resid 288 through 314
      removed outlier: 3.617A  pdb=" N   CYSA4 302 " --> pdb=" O   GLUA4 298 " (cutoff:3.500A)
    Processing helix  chain 'A4' and resid 326 through 353
      removed outlier: 3.643A  pdb=" N   THRA4 350 " --> pdb=" O   ASNA4 346 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   SERA4 351 " --> pdb=" O   ILEA4 347 " (cutoff:3.500A)
    Processing helix  chain 'A4' and resid 353 through 360
      removed outlier: 3.863A  pdb=" N   LEUA4 357 " --> pdb=" O   VALA4 353 " (cutoff:3.500A)
    Processing helix  chain 'A4' and resid 369 through 393
    Processing helix  chain 'A4' and resid 394 through 397
    Processing helix  chain 'A4' and resid 403 through 441
      removed outlier: 4.622A  pdb=" N   LYSA4 416 " --> pdb=" O   SERA4 412 " (cutoff:3.500A)
      removed outlier: 5.351A  pdb=" N   ASPA4 417 " --> pdb=" O   ARGA4 413 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ILEA4 428 " --> pdb=" O   META4 424 " (cutoff:3.500A)
    Processing helix  chain 'A4' and resid 444 through 448
    Processing helix  chain 'A4' and resid 449 through 463
    Processing helix  chain 'A4' and resid 466 through 474
      removed outlier: 3.538A  pdb=" N   ILEA4 470 " --> pdb=" O   ASNA4 466 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ASNA4 474 " --> pdb=" O   ILEA4 470 " (cutoff:3.500A)
    Processing helix  chain 'A4' and resid 476 through 491
      removed outlier: 3.884A  pdb=" N   ILEA4 480 " --> pdb=" O   VALA4 476 " (cutoff:3.500A)
    Processing helix  chain 'A4' and resid 493 through 513
      removed outlier: 4.237A  pdb=" N   PHEA4 497 " --> pdb=" O   LEUA4 493 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   LEUA4 498 " --> pdb=" O   LEUA4 494 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A1' and resid 134 through 136
      removed outlier: 6.644A  pdb=" N   LEUA1 145 " --> pdb=" O   ARGA1 241 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   THRA1 243 " --> pdb=" O   ARGA1 143 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   ARGA1 143 " --> pdb=" O   THRA1 243 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   ILEA1 245 " --> pdb=" O   ARGA1 141 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   ARGA1 141 " --> pdb=" O   ILEA1 245 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A1' and resid 134 through 136
    Processing sheet with id=AA3, first strand: chain 'A1' and resid 200 through 201
    Processing sheet with id=AA4, first strand: chain 'A2' and resid 134 through 136
      removed outlier: 6.676A  pdb=" N   LEUA2 145 " --> pdb=" O   ARGA2 241 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   THRA2 243 " --> pdb=" O   ARGA2 143 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   ARGA2 143 " --> pdb=" O   THRA2 243 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   ILEA2 245 " --> pdb=" O   ARGA2 141 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   ARGA2 141 " --> pdb=" O   ILEA2 245 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A2' and resid 134 through 136
    Processing sheet with id=AA6, first strand: chain 'A2' and resid 200 through 201
    Processing sheet with id=AA7, first strand: chain 'A3' and resid 134 through 136
      removed outlier: 6.677A  pdb=" N   LEUA3 145 " --> pdb=" O   ARGA3 241 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   THRA3 243 " --> pdb=" O   ARGA3 143 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   ARGA3 143 " --> pdb=" O   THRA3 243 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   ILEA3 245 " --> pdb=" O   ARGA3 141 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   ARGA3 141 " --> pdb=" O   ILEA3 245 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A3' and resid 134 through 136
    Processing sheet with id=AA9, first strand: chain 'A3' and resid 200 through 201
    Processing sheet with id=AB1, first strand: chain 'A4' and resid 134 through 136
      removed outlier: 6.645A  pdb=" N   LEUA4 145 " --> pdb=" O   ARGA4 241 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   THRA4 243 " --> pdb=" O   ARGA4 143 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   ARGA4 143 " --> pdb=" O   THRA4 243 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   ILEA4 245 " --> pdb=" O   ARGA4 141 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   ARGA4 141 " --> pdb=" O   ILEA4 245 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A4' and resid 134 through 136
    Processing sheet with id=AB3, first strand: chain 'A4' and resid 200 through 201

    921 hydrogen bonds defined for protein.
    2652 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: 6.24

  Time building geometry restraints manager: 3.10 seconds

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

  Histogram of bond lengths:
        0.88 -     1.07: 3152
        1.07 -     1.25: 14198
        1.25 -     1.44: 4774
        1.44 -     1.63: 8452
        1.63 -     1.82: 120
  Bond restraints: 30696
  Sorted by residual:
  bond pdb=" CD2 PHEA3 491 "
       pdb=" HD2 PHEA3 491 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" N   SERA3  95 "
       pdb=" H   SERA3  95 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" N   PHEA3 369 "
       pdb=" H   PHEA3 369 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" N   GLUA1 174 "
       pdb=" H   GLUA1 174 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" ND2 ASNA4 364 "
       pdb="HD21 ASNA4 364 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.66e+01
  ... (remaining 30691 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.60: 47567
        2.60 -     5.21: 5751
        5.21 -     7.81: 1714
        7.81 -    10.41: 64
       10.41 -    13.02: 32
  Bond angle restraints: 55128
  Sorted by residual:
  angle pdb=" CA  PHEA1 491 "
        pdb=" CB  PHEA1 491 "
        pdb=" CG  PHEA1 491 "
      ideal   model   delta    sigma   weight residual
     113.80  120.76   -6.96 1.00e+00 1.00e+00 4.85e+01
  angle pdb=" CA  PHEA4 491 "
        pdb=" CB  PHEA4 491 "
        pdb=" CG  PHEA4 491 "
      ideal   model   delta    sigma   weight residual
     113.80  120.45   -6.65 1.00e+00 1.00e+00 4.42e+01
  angle pdb=" CA  PHEA3 491 "
        pdb=" CB  PHEA3 491 "
        pdb=" CG  PHEA3 491 "
      ideal   model   delta    sigma   weight residual
     113.80  120.17   -6.37 1.00e+00 1.00e+00 4.06e+01
  angle pdb=" CA  PHEA2 491 "
        pdb=" CB  PHEA2 491 "
        pdb=" CG  PHEA2 491 "
      ideal   model   delta    sigma   weight residual
     113.80  120.05   -6.25 1.00e+00 1.00e+00 3.91e+01
  angle pdb=" N   PHEA4 131 "
        pdb=" CA  PHEA4 131 "
        pdb=" C   PHEA4 131 "
      ideal   model   delta    sigma   weight residual
     109.24  101.16    8.08 1.51e+00 4.39e-01 2.86e+01
  ... (remaining 55123 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.98: 13366
       16.98 -    33.97: 716
       33.97 -    50.95: 185
       50.95 -    67.94: 252
       67.94 -    84.92: 29
  Dihedral angle restraints: 14548
    sinusoidal: 7488
      harmonic: 7060
  Sorted by residual:
  dihedral pdb=" CB  CYSA4 152 "
           pdb=" SG  CYSA4 152 "
           pdb=" SG  CYSA4 165 "
           pdb=" CB  CYSA4 165 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.12  -52.12     1      1.00e+01 1.00e-02 3.71e+01
  dihedral pdb=" CB  CYSA3 152 "
           pdb=" SG  CYSA3 152 "
           pdb=" SG  CYSA3 165 "
           pdb=" CB  CYSA3 165 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  144.55  -51.55     1      1.00e+01 1.00e-02 3.63e+01
  dihedral pdb=" CA  ILEA2 130 "
           pdb=" C   ILEA2 130 "
           pdb=" N   PHEA2 131 "
           pdb=" CA  PHEA2 131 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.54   29.46     0      5.00e+00 4.00e-02 3.47e+01
  ... (remaining 14545 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1333
       0.068 -    0.135: 804
       0.135 -    0.203: 193
       0.203 -    0.270: 40
       0.270 -    0.338: 6
  Chirality restraints: 2376
  Sorted by residual:
  chirality pdb=" CA  PHEA1 426 "
            pdb=" N   PHEA1 426 "
            pdb=" C   PHEA1 426 "
            pdb=" CB  PHEA1 426 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.85e+00
  chirality pdb=" CA  PHEA4 426 "
            pdb=" N   PHEA4 426 "
            pdb=" C   PHEA4 426 "
            pdb=" CB  PHEA4 426 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.77e+00
  chirality pdb=" CA  PHEA3 426 "
            pdb=" N   PHEA3 426 "
            pdb=" C   PHEA3 426 "
            pdb=" CB  PHEA3 426 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.75e+00
  ... (remaining 2373 not shown)

  Planarity restraints: 4432
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARGA1 261 "   -0.430 9.50e-02 1.11e+02   2.13e-01 5.74e+02
        pdb=" NE  ARGA1 261 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  ARGA1 261 "    0.034 2.00e-02 2.50e+03
        pdb=" NH1 ARGA1 261 "   -0.031 2.00e-02 2.50e+03
        pdb=" NH2 ARGA1 261 "    0.127 2.00e-02 2.50e+03
        pdb="HH11 ARGA1 261 "   -0.124 2.00e-02 2.50e+03
        pdb="HH12 ARGA1 261 "    0.255 2.00e-02 2.50e+03
        pdb="HH21 ARGA1 261 "   -0.336 2.00e-02 2.50e+03
        pdb="HH22 ARGA1 261 "    0.098 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARGA2 261 "   -0.401 9.50e-02 1.11e+02   2.01e-01 5.28e+02
        pdb=" NE  ARGA2 261 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARGA2 261 "    0.031 2.00e-02 2.50e+03
        pdb=" NH1 ARGA2 261 "   -0.029 2.00e-02 2.50e+03
        pdb=" NH2 ARGA2 261 "    0.131 2.00e-02 2.50e+03
        pdb="HH11 ARGA2 261 "   -0.110 2.00e-02 2.50e+03
        pdb="HH12 ARGA2 261 "    0.237 2.00e-02 2.50e+03
        pdb="HH21 ARGA2 261 "   -0.327 2.00e-02 2.50e+03
        pdb="HH22 ARGA2 261 "    0.098 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRPA1 328 "    0.165 2.00e-02 2.50e+03   6.98e-02 1.95e+02
        pdb=" CG  TRPA1 328 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRPA1 328 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRPA1 328 "   -0.042 2.00e-02 2.50e+03
        pdb=" NE1 TRPA1 328 "   -0.066 2.00e-02 2.50e+03
        pdb=" CE2 TRPA1 328 "   -0.040 2.00e-02 2.50e+03
        pdb=" CE3 TRPA1 328 "   -0.068 2.00e-02 2.50e+03
        pdb=" CZ2 TRPA1 328 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRPA1 328 "   -0.026 2.00e-02 2.50e+03
        pdb=" CH2 TRPA1 328 "    0.043 2.00e-02 2.50e+03
        pdb=" HD1 TRPA1 328 "    0.033 2.00e-02 2.50e+03
        pdb=" HE1 TRPA1 328 "   -0.073 2.00e-02 2.50e+03
        pdb=" HE3 TRPA1 328 "   -0.098 2.00e-02 2.50e+03
        pdb=" HZ2 TRPA1 328 "    0.036 2.00e-02 2.50e+03
        pdb=" HZ3 TRPA1 328 "   -0.022 2.00e-02 2.50e+03
        pdb=" HH2 TRPA1 328 "    0.129 2.00e-02 2.50e+03
  ... (remaining 4429 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.18: 1557
        2.18 -     2.79: 53466
        2.79 -     3.39: 85335
        3.39 -     4.00: 116686
        4.00 -     4.60: 167283
  Nonbonded interactions: 424327
  Sorted by model distance:
  nonbonded pdb=" HH  TYRA4 169 "
            pdb=" OE2 GLUA4 174 "
     model   vdw
     1.578 2.450
  nonbonded pdb=" HH  TYRA2 169 "
            pdb=" OE2 GLUA2 174 "
     model   vdw
     1.579 2.450
  nonbonded pdb=" HH  TYRA3 169 "
            pdb=" OE2 GLUA3 174 "
     model   vdw
     1.581 2.450
  nonbonded pdb=" HG  SERA3 448 "
            pdb=" OE1 GLUA3 452 "
     model   vdw
     1.583 2.450
  nonbonded pdb=" HG1 THRA2 449 "
            pdb=" OE1 GLUA2 452 "
     model   vdw
     1.587 2.450
  ... (remaining 424322 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 'A1'
  selection = chain 'A2'
  selection = chain 'A3'
  selection = chain 'A4'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             54.690
  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:             0.190
  Extract box with map and model:          1.310
  Check model and map are aligned:         0.110
  Set scattering table:                    0.070
  Process input model:                     23.580
  Find NCS groups from input model:        0.420
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:5.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   85.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6735
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      :  0.013   0.041  15636  Z= 0.711
  Angle     :  1.663   8.082  21216  Z= 1.129
  Chirality :  0.085   0.338   2376
  Planarity :  0.014   0.130   2636
  Dihedral  : 13.116  84.919   5488
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  3.53 %
    Favored  : 96.11 %
  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 aren not related in a simple way.
  whole: -0.47 (0.18), residues: 1824
  helix: -0.12 (0.14), residues: 1024
  sheet:  0.95 (0.38), residues: 160
  loop : -0.75 (0.25), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.002   ARGA3 146 
 TYR   0.151   0.022   TYRA3  68 
 PHE   0.084   0.012   PHEA2 421 
 TRP   0.116   0.022   TRPA4 276 
 HIS   0.008   0.004   HISA4 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.01262 (15632)
  covalent geometry    : angle       1.66325 (21208)
  SS BOND              : bond        0.00195 (    4)
  SS BOND              : angle       1.80530 (    8)
  hydrogen bonds       : bond        0.16282 (  913)
  hydrogen bonds       : angle       6.50064 ( 2652)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 329
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 9
  residues processed: 335
  average time/residue: 0.9110
  time to fit residues: 346.1792
Evaluate side-chains
  204 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 195
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A1 residue  249 VAL
Chi-restraints excluded: chain A1 residue  461 ILE
Chi-restraints excluded: chain A2 residue  213 TYR
Chi-restraints excluded: chain A2 residue  343 ILE
Chi-restraints excluded: chain A2 residue  461 ILE
Chi-restraints excluded: chain A3 residue  130 ILE
Chi-restraints excluded: chain A3 residue  343 ILE
Chi-restraints excluded: chain A3 residue  461 ILE
Chi-restraints excluded: chain A4 residue  343 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    0.9980
   chunk 149 optimal weight:    3.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A1 495 ASN
A2 495 ASN
A3 399 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.203038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.171133 restraints weight = 44337.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 1.82
r_work: 0.3884 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3776 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7331
moved from start:          0.3188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  15636  Z= 0.144
  Angle     :  0.561   5.778  21216  Z= 0.319
  Chirality :  0.039   0.141   2376
  Planarity :  0.004   0.036   2636
  Dihedral  :  5.750  33.290   2037
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 2.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.24 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.19), residues: 1824
  helix:  1.37 (0.15), residues: 1040
  sheet:  0.18 (0.37), residues: 184
  loop : -0.46 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARGA4 143 
 TYR   0.024   0.002   TYRA3  68 
 PHE   0.026   0.002   PHEA2 421 
 TRP   0.011   0.001   TRPA4 235 
 HIS   0.003   0.001   HISA4 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (15632)
  covalent geometry    : angle       0.56097 (21208)
  SS BOND              : bond        0.00181 (    4)
  SS BOND              : angle       0.52257 (    8)
  hydrogen bonds       : bond        0.05332 (  913)
  hydrogen bonds       : angle       4.58812 ( 2652)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 230
  time to evaluate  : 0.606 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A1  330 CYS cc_start: 0.7777 (t) cc_final: 0.7370 (p)
REVERT: A2  330 CYS cc_start: 0.7845 (t) cc_final: 0.7567 (p)
REVERT: A2  386 THR cc_start: 0.6953 (p) cc_final: 0.6743 (m)
REVERT: A2  442 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8245 (t)
REVERT: A3  311 GLU cc_start: 0.5409 (OUTLIER) cc_final: 0.4743 (tt0)
REVERT: A3  330 CYS cc_start: 0.7737 (t) cc_final: 0.7481 (p)
REVERT: A4  292 PHE cc_start: 0.6388 (m-80) cc_final: 0.6165 (m-80)
REVERT: A4  330 CYS cc_start: 0.7757 (t) cc_final: 0.7389 (p)
  outliers start: 28
  outliers final: 15
  residues processed: 252
  average time/residue: 0.7681
  time to fit residues: 224.3836
Evaluate side-chains
  188 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 171
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A1 residue  248 SER
Chi-restraints excluded: chain A1 residue  249 VAL
Chi-restraints excluded: chain A1 residue  343 ILE
Chi-restraints excluded: chain A2 residue  190 THR
Chi-restraints excluded: chain A2 residue  343 ILE
Chi-restraints excluded: chain A2 residue  442 THR
Chi-restraints excluded: chain A2 residue  461 ILE
Chi-restraints excluded: chain A3 residue  130 ILE
Chi-restraints excluded: chain A3 residue  173 SER
Chi-restraints excluded: chain A3 residue  198 SER
Chi-restraints excluded: chain A3 residue  297 CYS
Chi-restraints excluded: chain A3 residue  311 GLU
Chi-restraints excluded: chain A3 residue  343 ILE
Chi-restraints excluded: chain A3 residue  364 ASN
Chi-restraints excluded: chain A4 residue  297 CYS
Chi-restraints excluded: chain A4 residue  343 ILE
Chi-restraints excluded: chain A4 residue  461 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 183 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 171 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 172 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   chunk 111 optimal weight:    3.9990
   chunk 118 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 116 optimal weight:    4.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A1 434 GLN
A2 399 ASN
A3 399 ASN
A3 502 ASN
A4 502 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.194455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.161848 restraints weight = 44619.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 1.81
r_work: 0.3790 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3687 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.4024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  15636  Z= 0.202
  Angle     :  0.583   5.465  21216  Z= 0.329
  Chirality :  0.041   0.142   2376
  Planarity :  0.005   0.045   2636
  Dihedral  :  5.606  40.389   2031
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 12.38 %
    Favored  : 84.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.19), residues: 1824
  helix:  1.50 (0.15), residues: 1044
  sheet: -0.05 (0.37), residues: 184
  loop : -0.55 (0.26), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARGA1 143 
 TYR   0.026   0.002   TYRA4  68 
 PHE   0.023   0.002   PHEA2 421 
 TRP   0.008   0.002   TRPA2 375 
 HIS   0.006   0.003   HISA3 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 (15632)
  covalent geometry    : angle       0.58299 (21208)
  SS BOND              : bond        0.00226 (    4)
  SS BOND              : angle       0.55005 (    8)
  hydrogen bonds       : bond        0.05375 (  913)
  hydrogen bonds       : angle       4.65350 ( 2652)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 190
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A1   60 TYR cc_start: 0.4202 (OUTLIER) cc_final: 0.3592 (t80)
REVERT: A1  330 CYS cc_start: 0.7766 (t) cc_final: 0.7394 (p)
REVERT: A2  330 CYS cc_start: 0.7752 (t) cc_final: 0.7552 (p)
REVERT: A2  333 VAL cc_start: 0.7717 (OUTLIER) cc_final: 0.7496 (t)
REVERT: A2  386 THR cc_start: 0.7046 (p) cc_final: 0.6822 (m)
REVERT: A3  171 VAL cc_start: 0.6415 (OUTLIER) cc_final: 0.6172 (t)
REVERT: A3  311 GLU cc_start: 0.5263 (OUTLIER) cc_final: 0.3788 (mp0)
REVERT: A3  330 CYS cc_start: 0.7729 (t) cc_final: 0.7503 (p)
REVERT: A3  472 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7330 (tp30)
REVERT: A4  171 VAL cc_start: 0.6372 (OUTLIER) cc_final: 0.6141 (t)
REVERT: A4  330 CYS cc_start: 0.7789 (t) cc_final: 0.7523 (p)
REVERT: A4  472 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7297 (tp30)
  outliers start: 49
  outliers final: 29
  residues processed: 229
  average time/residue: 0.7384
  time to fit residues: 196.2489
Evaluate side-chains
  195 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 159
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A1 residue   60 TYR
Chi-restraints excluded: chain A1 residue  190 THR
Chi-restraints excluded: chain A1 residue  248 SER
Chi-restraints excluded: chain A1 residue  249 VAL
Chi-restraints excluded: chain A1 residue  275 SER
Chi-restraints excluded: chain A1 residue  343 ILE
Chi-restraints excluded: chain A1 residue  456 THR
Chi-restraints excluded: chain A1 residue  461 ILE
Chi-restraints excluded: chain A2 residue  190 THR
Chi-restraints excluded: chain A2 residue  248 SER
Chi-restraints excluded: chain A2 residue  275 SER
Chi-restraints excluded: chain A2 residue  333 VAL
Chi-restraints excluded: chain A2 residue  343 ILE
Chi-restraints excluded: chain A2 residue  418 LEU
Chi-restraints excluded: chain A2 residue  442 THR
Chi-restraints excluded: chain A2 residue  461 ILE
Chi-restraints excluded: chain A3 residue  130 ILE
Chi-restraints excluded: chain A3 residue  171 VAL
Chi-restraints excluded: chain A3 residue  173 SER
Chi-restraints excluded: chain A3 residue  198 SER
Chi-restraints excluded: chain A3 residue  248 SER
Chi-restraints excluded: chain A3 residue  275 SER
Chi-restraints excluded: chain A3 residue  311 GLU
Chi-restraints excluded: chain A3 residue  343 ILE
Chi-restraints excluded: chain A3 residue  364 ASN
Chi-restraints excluded: chain A3 residue  461 ILE
Chi-restraints excluded: chain A3 residue  472 GLU
Chi-restraints excluded: chain A4 residue  171 VAL
Chi-restraints excluded: chain A4 residue  185 THR
Chi-restraints excluded: chain A4 residue  248 SER
Chi-restraints excluded: chain A4 residue  249 VAL
Chi-restraints excluded: chain A4 residue  297 CYS
Chi-restraints excluded: chain A4 residue  343 ILE
Chi-restraints excluded: chain A4 residue  442 THR
Chi-restraints excluded: chain A4 residue  461 ILE
Chi-restraints excluded: chain A4 residue  472 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 183 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 150 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 46 optimal weight:    9.9990
   chunk 102 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 177 optimal weight:    2.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A1 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2 399 ASN
A3 399 ASN
** A4 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A4 399 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.191962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.159689 restraints weight = 44488.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3867 rms_B_bonded: 1.78
r_work: 0.3784 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3684 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.4626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  15636  Z= 0.244
  Angle     :  0.616   5.733  21216  Z= 0.347
  Chirality :  0.042   0.145   2376
  Planarity :  0.005   0.046   2636
  Dihedral  :  5.732  49.752   2031
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 12.80 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.19), residues: 1824
  helix:  1.32 (0.15), residues: 1048
  sheet:  0.06 (0.38), residues: 184
  loop : -0.72 (0.26), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARGA1 143 
 TYR   0.017   0.003   TYRA1  48 
 PHE   0.024   0.002   PHEA2 421 
 TRP   0.010   0.002   TRPA1 187 
 HIS   0.007   0.003   HISA2 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00573 (15632)
  covalent geometry    : angle       0.61620 (21208)
  SS BOND              : bond        0.00167 (    4)
  SS BOND              : angle       0.47492 (    8)
  hydrogen bonds       : bond        0.05523 (  913)
  hydrogen bonds       : angle       4.72642 ( 2652)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 175
  time to evaluate  : 0.638 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A1   60 TYR cc_start: 0.4538 (OUTLIER) cc_final: 0.2890 (t80)
REVERT: A1  330 CYS cc_start: 0.7686 (t) cc_final: 0.7423 (p)
REVERT: A1  471 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7443 (tt0)
REVERT: A2   60 TYR cc_start: 0.4320 (OUTLIER) cc_final: 0.2804 (t80)
REVERT: A2  333 VAL cc_start: 0.7730 (OUTLIER) cc_final: 0.7479 (t)
REVERT: A3   60 TYR cc_start: 0.4355 (OUTLIER) cc_final: 0.2845 (t80)
REVERT: A3  333 VAL cc_start: 0.7670 (OUTLIER) cc_final: 0.7402 (t)
REVERT: A4   60 TYR cc_start: 0.4272 (OUTLIER) cc_final: 0.2808 (t80)
REVERT: A4  330 CYS cc_start: 0.7738 (t) cc_final: 0.7529 (p)
REVERT: A4  469 GLU cc_start: 0.7284 (pt0) cc_final: 0.6830 (mm-30)
  outliers start: 69
  outliers final: 46
  residues processed: 230
  average time/residue: 0.6932
  time to fit residues: 187.6137
Evaluate side-chains
  223 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 170
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A1 residue   60 TYR
Chi-restraints excluded: chain A1 residue  134 ASN
Chi-restraints excluded: chain A1 residue  139 VAL
Chi-restraints excluded: chain A1 residue  171 VAL
Chi-restraints excluded: chain A1 residue  190 THR
Chi-restraints excluded: chain A1 residue  248 SER
Chi-restraints excluded: chain A1 residue  249 VAL
Chi-restraints excluded: chain A1 residue  254 ILE
Chi-restraints excluded: chain A1 residue  275 SER
Chi-restraints excluded: chain A1 residue  343 ILE
Chi-restraints excluded: chain A1 residue  461 ILE
Chi-restraints excluded: chain A1 residue  471 GLU
Chi-restraints excluded: chain A2 residue   60 TYR
Chi-restraints excluded: chain A2 residue   89 THR
Chi-restraints excluded: chain A2 residue  134 ASN
Chi-restraints excluded: chain A2 residue  139 VAL
Chi-restraints excluded: chain A2 residue  171 VAL
Chi-restraints excluded: chain A2 residue  190 THR
Chi-restraints excluded: chain A2 residue  248 SER
Chi-restraints excluded: chain A2 residue  249 VAL
Chi-restraints excluded: chain A2 residue  254 ILE
Chi-restraints excluded: chain A2 residue  275 SER
Chi-restraints excluded: chain A2 residue  333 VAL
Chi-restraints excluded: chain A2 residue  343 ILE
Chi-restraints excluded: chain A2 residue  442 THR
Chi-restraints excluded: chain A2 residue  461 ILE
Chi-restraints excluded: chain A3 residue   60 TYR
Chi-restraints excluded: chain A3 residue  130 ILE
Chi-restraints excluded: chain A3 residue  139 VAL
Chi-restraints excluded: chain A3 residue  171 VAL
Chi-restraints excluded: chain A3 residue  173 SER
Chi-restraints excluded: chain A3 residue  198 SER
Chi-restraints excluded: chain A3 residue  199 SER
Chi-restraints excluded: chain A3 residue  248 SER
Chi-restraints excluded: chain A3 residue  254 ILE
Chi-restraints excluded: chain A3 residue  275 SER
Chi-restraints excluded: chain A3 residue  311 GLU
Chi-restraints excluded: chain A3 residue  333 VAL
Chi-restraints excluded: chain A3 residue  343 ILE
Chi-restraints excluded: chain A3 residue  364 ASN
Chi-restraints excluded: chain A3 residue  461 ILE
Chi-restraints excluded: chain A4 residue   60 TYR
Chi-restraints excluded: chain A4 residue  134 ASN
Chi-restraints excluded: chain A4 residue  139 VAL
Chi-restraints excluded: chain A4 residue  171 VAL
Chi-restraints excluded: chain A4 residue  173 SER
Chi-restraints excluded: chain A4 residue  185 THR
Chi-restraints excluded: chain A4 residue  248 SER
Chi-restraints excluded: chain A4 residue  254 ILE
Chi-restraints excluded: chain A4 residue  275 SER
Chi-restraints excluded: chain A4 residue  343 ILE
Chi-restraints excluded: chain A4 residue  442 THR
Chi-restraints excluded: chain A4 residue  461 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 175 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 171 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A1 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2 399 ASN
A3 399 ASN
** A4 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.193630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.161443 restraints weight = 44636.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3888 rms_B_bonded: 1.78
r_work: 0.3805 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3706 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.4865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15636  Z= 0.173
  Angle     :  0.537   4.734  21216  Z= 0.301
  Chirality :  0.039   0.141   2376
  Planarity :  0.005   0.047   2636
  Dihedral  :  5.429  50.520   2031
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 14.29 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.19), residues: 1824
  helix:  1.57 (0.15), residues: 1044
  sheet: -0.05 (0.38), residues: 184
  loop : -0.67 (0.26), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARGA3 475 
 TYR   0.017   0.002   TYRA1  48 
 PHE   0.021   0.002   PHEA4 421 
 TRP   0.008   0.001   TRPA3 375 
 HIS   0.005   0.002   HISA3 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (15632)
  covalent geometry    : angle       0.53669 (21208)
  SS BOND              : bond        0.00213 (    4)
  SS BOND              : angle       0.51794 (    8)
  hydrogen bonds       : bond        0.04930 (  913)
  hydrogen bonds       : angle       4.52999 ( 2652)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 185
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A1   60 TYR cc_start: 0.4528 (OUTLIER) cc_final: 0.2822 (t80)
REVERT: A1  330 CYS cc_start: 0.7718 (t) cc_final: 0.7490 (p)
REVERT: A1  471 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7380 (tt0)
REVERT: A2   60 TYR cc_start: 0.4365 (OUTLIER) cc_final: 0.2776 (t80)
REVERT: A2  502 ASN cc_start: 0.7772 (t0) cc_final: 0.7154 (m110)
REVERT: A3   60 TYR cc_start: 0.4337 (OUTLIER) cc_final: 0.2797 (t80)
REVERT: A4   60 TYR cc_start: 0.4279 (OUTLIER) cc_final: 0.2780 (t80)
REVERT: A4  469 GLU cc_start: 0.7240 (pt0) cc_final: 0.6809 (mm-30)
  outliers start: 52
  outliers final: 35
  residues processed: 228
  average time/residue: 0.6137
  time to fit residues: 168.1091
Evaluate side-chains
  206 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 166
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A1 residue   60 TYR
Chi-restraints excluded: chain A1 residue  190 THR
Chi-restraints excluded: chain A1 residue  248 SER
Chi-restraints excluded: chain A1 residue  249 VAL
Chi-restraints excluded: chain A1 residue  254 ILE
Chi-restraints excluded: chain A1 residue  275 SER
Chi-restraints excluded: chain A1 residue  343 ILE
Chi-restraints excluded: chain A1 residue  461 ILE
Chi-restraints excluded: chain A1 residue  471 GLU
Chi-restraints excluded: chain A2 residue   60 TYR
Chi-restraints excluded: chain A2 residue  139 VAL
Chi-restraints excluded: chain A2 residue  171 VAL
Chi-restraints excluded: chain A2 residue  190 THR
Chi-restraints excluded: chain A2 residue  248 SER
Chi-restraints excluded: chain A2 residue  254 ILE
Chi-restraints excluded: chain A2 residue  275 SER
Chi-restraints excluded: chain A2 residue  343 ILE
Chi-restraints excluded: chain A3 residue   60 TYR
Chi-restraints excluded: chain A3 residue  130 ILE
Chi-restraints excluded: chain A3 residue  134 ASN
Chi-restraints excluded: chain A3 residue  139 VAL
Chi-restraints excluded: chain A3 residue  173 SER
Chi-restraints excluded: chain A3 residue  198 SER
Chi-restraints excluded: chain A3 residue  199 SER
Chi-restraints excluded: chain A3 residue  248 SER
Chi-restraints excluded: chain A3 residue  275 SER
Chi-restraints excluded: chain A3 residue  311 GLU
Chi-restraints excluded: chain A3 residue  343 ILE
Chi-restraints excluded: chain A3 residue  364 ASN
Chi-restraints excluded: chain A3 residue  461 ILE
Chi-restraints excluded: chain A4 residue   60 TYR
Chi-restraints excluded: chain A4 residue  139 VAL
Chi-restraints excluded: chain A4 residue  151 SER
Chi-restraints excluded: chain A4 residue  171 VAL
Chi-restraints excluded: chain A4 residue  173 SER
Chi-restraints excluded: chain A4 residue  248 SER
Chi-restraints excluded: chain A4 residue  254 ILE
Chi-restraints excluded: chain A4 residue  275 SER
Chi-restraints excluded: chain A4 residue  343 ILE
Chi-restraints excluded: chain A4 residue  461 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 121 optimal weight:    5.9990
   chunk 161 optimal weight:    2.9990
   chunk 155 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 70 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9990
   chunk 167 optimal weight:    6.9990
   chunk 91 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A1 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3 502 ASN
** A4 251 ASN ** 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 = 0.4151 r_free = 0.4151 target = 0.190124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.157859 restraints weight = 44651.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3835 rms_B_bonded: 1.80
r_work: 0.3749 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3645 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.5051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066  15636  Z= 0.232
  Angle     :  0.593   5.529  21216  Z= 0.333
  Chirality :  0.041   0.144   2376
  Planarity :  0.005   0.049   2636
  Dihedral  :  5.590  56.745   2029
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 13.88 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.19), residues: 1824
  helix:  1.42 (0.15), residues: 1048
  sheet:  0.01 (0.37), residues: 184
  loop : -0.77 (0.26), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARGA2 475 
 TYR   0.018   0.002   TYRA1  48 
 PHE   0.021   0.002   PHEA4 421 
 TRP   0.007   0.002   TRPA4 276 
 HIS   0.007   0.003   HISA2 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00546 (15632)
  covalent geometry    : angle       0.59299 (21208)
  SS BOND              : bond        0.00275 (    4)
  SS BOND              : angle       0.41329 (    8)
  hydrogen bonds       : bond        0.05361 (  913)
  hydrogen bonds       : angle       4.68746 ( 2652)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 171
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A1   60 TYR cc_start: 0.4580 (OUTLIER) cc_final: 0.2854 (t80)
REVERT: A1  330 CYS cc_start: 0.7688 (t) cc_final: 0.7460 (p)
REVERT: A1  471 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7439 (tt0)
REVERT: A2   60 TYR cc_start: 0.4438 (OUTLIER) cc_final: 0.2777 (t80)
REVERT: A3   60 TYR cc_start: 0.4426 (OUTLIER) cc_final: 0.2794 (t80)
REVERT: A3  402 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6919 (mtm-85)
REVERT: A4   60 TYR cc_start: 0.4433 (OUTLIER) cc_final: 0.2825 (t80)
REVERT: A4  163 LYS cc_start: 0.6004 (mttt) cc_final: 0.4968 (mmmt)
REVERT: A4  469 GLU cc_start: 0.7222 (pt0) cc_final: 0.6685 (mp0)
  outliers start: 72
  outliers final: 49
  residues processed: 232
  average time/residue: 0.6594
  time to fit residues: 181.5395
Evaluate side-chains
  221 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 166
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A1 residue   60 TYR
Chi-restraints excluded: chain A1 residue   83 VAL
Chi-restraints excluded: chain A1 residue  134 ASN
Chi-restraints excluded: chain A1 residue  139 VAL
Chi-restraints excluded: chain A1 residue  157 ASP
Chi-restraints excluded: chain A1 residue  171 VAL
Chi-restraints excluded: chain A1 residue  190 THR
Chi-restraints excluded: chain A1 residue  248 SER
Chi-restraints excluded: chain A1 residue  249 VAL
Chi-restraints excluded: chain A1 residue  275 SER
Chi-restraints excluded: chain A1 residue  343 ILE
Chi-restraints excluded: chain A1 residue  461 ILE
Chi-restraints excluded: chain A1 residue  471 GLU
Chi-restraints excluded: chain A2 residue   60 TYR
Chi-restraints excluded: chain A2 residue   83 VAL
Chi-restraints excluded: chain A2 residue   89 THR
Chi-restraints excluded: chain A2 residue  134 ASN
Chi-restraints excluded: chain A2 residue  139 VAL
Chi-restraints excluded: chain A2 residue  171 VAL
Chi-restraints excluded: chain A2 residue  190 THR
Chi-restraints excluded: chain A2 residue  248 SER
Chi-restraints excluded: chain A2 residue  254 ILE
Chi-restraints excluded: chain A2 residue  275 SER
Chi-restraints excluded: chain A2 residue  442 THR
Chi-restraints excluded: chain A2 residue  461 ILE
Chi-restraints excluded: chain A3 residue   60 TYR
Chi-restraints excluded: chain A3 residue   83 VAL
Chi-restraints excluded: chain A3 residue  130 ILE
Chi-restraints excluded: chain A3 residue  134 ASN
Chi-restraints excluded: chain A3 residue  139 VAL
Chi-restraints excluded: chain A3 residue  171 VAL
Chi-restraints excluded: chain A3 residue  173 SER
Chi-restraints excluded: chain A3 residue  198 SER
Chi-restraints excluded: chain A3 residue  248 SER
Chi-restraints excluded: chain A3 residue  275 SER
Chi-restraints excluded: chain A3 residue  311 GLU
Chi-restraints excluded: chain A3 residue  364 ASN
Chi-restraints excluded: chain A3 residue  402 ARG
Chi-restraints excluded: chain A3 residue  461 ILE
Chi-restraints excluded: chain A4 residue   60 TYR
Chi-restraints excluded: chain A4 residue   83 VAL
Chi-restraints excluded: chain A4 residue  134 ASN
Chi-restraints excluded: chain A4 residue  139 VAL
Chi-restraints excluded: chain A4 residue  151 SER
Chi-restraints excluded: chain A4 residue  157 ASP
Chi-restraints excluded: chain A4 residue  171 VAL
Chi-restraints excluded: chain A4 residue  173 SER
Chi-restraints excluded: chain A4 residue  185 THR
Chi-restraints excluded: chain A4 residue  248 SER
Chi-restraints excluded: chain A4 residue  254 ILE
Chi-restraints excluded: chain A4 residue  275 SER
Chi-restraints excluded: chain A4 residue  311 GLU
Chi-restraints excluded: chain A4 residue  343 ILE
Chi-restraints excluded: chain A4 residue  442 THR
Chi-restraints excluded: chain A4 residue  461 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 94 optimal weight:    8.9990
   chunk 48 optimal weight:    5.9990
   chunk 180 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 129 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 112 optimal weight:    3.9990
   chunk 105 optimal weight:    2.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A1 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2 399 ASN
** A4 251 ASN ** 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 = 0.4147 r_free = 0.4147 target = 0.189642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.157428 restraints weight = 44898.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3831 rms_B_bonded: 1.80
r_work: 0.3746 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3642 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.5172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  15636  Z= 0.229
  Angle     :  0.587   5.557  21216  Z= 0.330
  Chirality :  0.041   0.143   2376
  Planarity :  0.005   0.049   2636
  Dihedral  :  5.503  56.713   2025
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 14.59 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.19), residues: 1824
  helix:  1.38 (0.15), residues: 1052
  sheet:  0.02 (0.37), residues: 184
  loop : -0.77 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARGA4  72 
 TYR   0.018   0.002   TYRA1  48 
 PHE   0.021   0.002   PHEA4 421 
 TRP   0.007   0.002   TRPA4 276 
 HIS   0.006   0.003   HISA1 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00534 (15632)
  covalent geometry    : angle       0.58728 (21208)
  SS BOND              : bond        0.00313 (    4)
  SS BOND              : angle       0.46453 (    8)
  hydrogen bonds       : bond        0.05312 (  913)
  hydrogen bonds       : angle       4.68836 ( 2652)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 173
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A1   60 TYR cc_start: 0.4564 (OUTLIER) cc_final: 0.2821 (t80)
REVERT: A1  330 CYS cc_start: 0.7660 (t) cc_final: 0.7440 (p)
REVERT: A1  471 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7422 (tt0)
REVERT: A1  498 LEU cc_start: 0.8045 (tt) cc_final: 0.7715 (mp)
REVERT: A2   60 TYR cc_start: 0.4468 (OUTLIER) cc_final: 0.2761 (t80)
REVERT: A3   60 TYR cc_start: 0.4436 (OUTLIER) cc_final: 0.2801 (t80)
REVERT: A3  163 LYS cc_start: 0.6038 (mttt) cc_final: 0.4936 (mmmt)
REVERT: A3  281 LEU cc_start: 0.5874 (OUTLIER) cc_final: 0.5475 (mt)
REVERT: A3  402 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6878 (mtm-85)
REVERT: A4   60 TYR cc_start: 0.4433 (OUTLIER) cc_final: 0.2784 (t80)
REVERT: A4  163 LYS cc_start: 0.5969 (mttt) cc_final: 0.4940 (mmmt)
REVERT: A4  194 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7352 (t0)
REVERT: A4  402 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6950 (mtm-85)
REVERT: A4  469 GLU cc_start: 0.7184 (pt0) cc_final: 0.6914 (mt-10)
  outliers start: 72
  outliers final: 51
  residues processed: 233
  average time/residue: 0.6672
  time to fit residues: 185.0616
Evaluate side-chains
  226 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 166
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A1 residue   60 TYR
Chi-restraints excluded: chain A1 residue   83 VAL
Chi-restraints excluded: chain A1 residue   89 THR
Chi-restraints excluded: chain A1 residue  134 ASN
Chi-restraints excluded: chain A1 residue  139 VAL
Chi-restraints excluded: chain A1 residue  157 ASP
Chi-restraints excluded: chain A1 residue  190 THR
Chi-restraints excluded: chain A1 residue  248 SER
Chi-restraints excluded: chain A1 residue  249 VAL
Chi-restraints excluded: chain A1 residue  275 SER
Chi-restraints excluded: chain A1 residue  343 ILE
Chi-restraints excluded: chain A1 residue  461 ILE
Chi-restraints excluded: chain A1 residue  471 GLU
Chi-restraints excluded: chain A2 residue   60 TYR
Chi-restraints excluded: chain A2 residue   83 VAL
Chi-restraints excluded: chain A2 residue   89 THR
Chi-restraints excluded: chain A2 residue  134 ASN
Chi-restraints excluded: chain A2 residue  139 VAL
Chi-restraints excluded: chain A2 residue  171 VAL
Chi-restraints excluded: chain A2 residue  190 THR
Chi-restraints excluded: chain A2 residue  248 SER
Chi-restraints excluded: chain A2 residue  275 SER
Chi-restraints excluded: chain A2 residue  343 ILE
Chi-restraints excluded: chain A2 residue  442 THR
Chi-restraints excluded: chain A2 residue  461 ILE
Chi-restraints excluded: chain A3 residue   60 TYR
Chi-restraints excluded: chain A3 residue   83 VAL
Chi-restraints excluded: chain A3 residue   89 THR
Chi-restraints excluded: chain A3 residue  130 ILE
Chi-restraints excluded: chain A3 residue  134 ASN
Chi-restraints excluded: chain A3 residue  139 VAL
Chi-restraints excluded: chain A3 residue  171 VAL
Chi-restraints excluded: chain A3 residue  173 SER
Chi-restraints excluded: chain A3 residue  198 SER
Chi-restraints excluded: chain A3 residue  248 SER
Chi-restraints excluded: chain A3 residue  275 SER
Chi-restraints excluded: chain A3 residue  281 LEU
Chi-restraints excluded: chain A3 residue  311 GLU
Chi-restraints excluded: chain A3 residue  343 ILE
Chi-restraints excluded: chain A3 residue  364 ASN
Chi-restraints excluded: chain A3 residue  402 ARG
Chi-restraints excluded: chain A3 residue  461 ILE
Chi-restraints excluded: chain A4 residue   60 TYR
Chi-restraints excluded: chain A4 residue   83 VAL
Chi-restraints excluded: chain A4 residue   89 THR
Chi-restraints excluded: chain A4 residue  134 ASN
Chi-restraints excluded: chain A4 residue  139 VAL
Chi-restraints excluded: chain A4 residue  151 SER
Chi-restraints excluded: chain A4 residue  157 ASP
Chi-restraints excluded: chain A4 residue  171 VAL
Chi-restraints excluded: chain A4 residue  173 SER
Chi-restraints excluded: chain A4 residue  185 THR
Chi-restraints excluded: chain A4 residue  194 ASP
Chi-restraints excluded: chain A4 residue  248 SER
Chi-restraints excluded: chain A4 residue  275 SER
Chi-restraints excluded: chain A4 residue  311 GLU
Chi-restraints excluded: chain A4 residue  343 ILE
Chi-restraints excluded: chain A4 residue  402 ARG
Chi-restraints excluded: chain A4 residue  442 THR
Chi-restraints excluded: chain A4 residue  461 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 134 optimal weight:    0.8980
   chunk 17 optimal weight:    0.2980
   chunk 1 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 151 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9980
   chunk 129 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 171 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A1 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1 457 GLN
A2 399 ASN
A2 457 GLN
A3 457 GLN
A3 502 ASN
A4 144 GLN
A4 457 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.194170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.162161 restraints weight = 44571.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3889 rms_B_bonded: 1.78
r_work: 0.3805 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3705 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.5291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  15636  Z= 0.117
  Angle     :  0.475   4.485  21216  Z= 0.264
  Chirality :  0.037   0.138   2376
  Planarity :  0.004   0.046   2636
  Dihedral  :  4.995  55.367   2025
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.39 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.22 (0.19), residues: 1824
  helix:  1.82 (0.15), residues: 1048
  sheet: -0.25 (0.36), residues: 184
  loop : -0.63 (0.26), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARGA2 285 
 TYR   0.024   0.002   TYRA1  68 
 PHE   0.019   0.001   PHEA4 421 
 TRP   0.008   0.001   TRPA4 276 
 HIS   0.003   0.001   HISA1 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (15632)
  covalent geometry    : angle       0.47493 (21208)
  SS BOND              : bond        0.00209 (    4)
  SS BOND              : angle       0.57504 (    8)
  hydrogen bonds       : bond        0.04378 (  913)
  hydrogen bonds       : angle       4.31491 ( 2652)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 170
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A1   60 TYR cc_start: 0.4485 (OUTLIER) cc_final: 0.2776 (t80)
REVERT: A1  471 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7293 (tt0)
REVERT: A1  498 LEU cc_start: 0.8026 (tt) cc_final: 0.7744 (mp)
REVERT: A2   60 TYR cc_start: 0.4356 (OUTLIER) cc_final: 0.2724 (t80)
REVERT: A2  502 ASN cc_start: 0.7670 (t0) cc_final: 0.7204 (m110)
REVERT: A3   60 TYR cc_start: 0.4248 (OUTLIER) cc_final: 0.2726 (t80)
REVERT: A3  281 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5374 (mt)
REVERT: A3  402 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6719 (mtm-85)
REVERT: A4   60 TYR cc_start: 0.4293 (OUTLIER) cc_final: 0.2746 (t80)
REVERT: A4  163 LYS cc_start: 0.5958 (mttt) cc_final: 0.4893 (mmmt)
REVERT: A4  311 GLU cc_start: 0.5022 (OUTLIER) cc_final: 0.3125 (mp0)
REVERT: A4  402 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6807 (mtm-85)
REVERT: A4  469 GLU cc_start: 0.7120 (pt0) cc_final: 0.6884 (mt-10)
  outliers start: 41
  outliers final: 22
  residues processed: 204
  average time/residue: 0.6626
  time to fit residues: 161.5255
Evaluate side-chains
  196 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 165
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A1 residue   60 TYR
Chi-restraints excluded: chain A1 residue  249 VAL
Chi-restraints excluded: chain A1 residue  275 SER
Chi-restraints excluded: chain A1 residue  343 ILE
Chi-restraints excluded: chain A1 residue  461 ILE
Chi-restraints excluded: chain A1 residue  471 GLU
Chi-restraints excluded: chain A2 residue   60 TYR
Chi-restraints excluded: chain A2 residue  139 VAL
Chi-restraints excluded: chain A2 residue  248 SER
Chi-restraints excluded: chain A2 residue  275 SER
Chi-restraints excluded: chain A2 residue  330 CYS
Chi-restraints excluded: chain A2 residue  343 ILE
Chi-restraints excluded: chain A3 residue   60 TYR
Chi-restraints excluded: chain A3 residue  130 ILE
Chi-restraints excluded: chain A3 residue  139 VAL
Chi-restraints excluded: chain A3 residue  172 SER
Chi-restraints excluded: chain A3 residue  275 SER
Chi-restraints excluded: chain A3 residue  281 LEU
Chi-restraints excluded: chain A3 residue  297 CYS
Chi-restraints excluded: chain A3 residue  311 GLU
Chi-restraints excluded: chain A3 residue  343 ILE
Chi-restraints excluded: chain A3 residue  402 ARG
Chi-restraints excluded: chain A3 residue  461 ILE
Chi-restraints excluded: chain A4 residue   60 TYR
Chi-restraints excluded: chain A4 residue  139 VAL
Chi-restraints excluded: chain A4 residue  173 SER
Chi-restraints excluded: chain A4 residue  248 SER
Chi-restraints excluded: chain A4 residue  275 SER
Chi-restraints excluded: chain A4 residue  311 GLU
Chi-restraints excluded: chain A4 residue  402 ARG
Chi-restraints excluded: chain A4 residue  461 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 156 optimal weight:    0.3980
   chunk 54 optimal weight:    0.7980
   chunk 160 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A1 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3 346 ASN
A4 144 GLN
** A4 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.193957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.161952 restraints weight = 44399.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 1.77
r_work: 0.3801 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3700 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.5339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15636  Z= 0.126
  Angle     :  0.476   4.507  21216  Z= 0.265
  Chirality :  0.038   0.139   2376
  Planarity :  0.004   0.044   2636
  Dihedral  :  4.860  51.573   2023
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.33 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.33 (0.19), residues: 1824
  helix:  1.92 (0.15), residues: 1048
  sheet: -0.26 (0.36), residues: 184
  loop : -0.60 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARGA4 475 
 TYR   0.023   0.002   TYRA1  68 
 PHE   0.019   0.001   PHEA4 421 
 TRP   0.007   0.001   TRPA4 276 
 HIS   0.003   0.001   HISA1 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (15632)
  covalent geometry    : angle       0.47596 (21208)
  SS BOND              : bond        0.00160 (    4)
  SS BOND              : angle       0.48038 (    8)
  hydrogen bonds       : bond        0.04339 (  913)
  hydrogen bonds       : angle       4.29201 ( 2652)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 169
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A1   60 TYR cc_start: 0.4427 (OUTLIER) cc_final: 0.2712 (t80)
REVERT: A1  163 LYS cc_start: 0.5981 (mttt) cc_final: 0.4997 (mmmt)
REVERT: A1  471 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7317 (tt0)
REVERT: A1  498 LEU cc_start: 0.8008 (tt) cc_final: 0.7772 (mp)
REVERT: A2   60 TYR cc_start: 0.4352 (OUTLIER) cc_final: 0.2726 (t80)
REVERT: A2  502 ASN cc_start: 0.7659 (t0) cc_final: 0.7208 (m110)
REVERT: A3   60 TYR cc_start: 0.4220 (OUTLIER) cc_final: 0.2709 (t80)
REVERT: A3  163 LYS cc_start: 0.5990 (mttt) cc_final: 0.4875 (mmmt)
REVERT: A3  402 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6720 (mtm-85)
REVERT: A4   60 TYR cc_start: 0.4296 (OUTLIER) cc_final: 0.2726 (t80)
REVERT: A4  163 LYS cc_start: 0.5944 (mttt) cc_final: 0.4873 (mmmt)
REVERT: A4  311 GLU cc_start: 0.4990 (OUTLIER) cc_final: 0.3104 (mp0)
REVERT: A4  402 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6789 (mtm-85)
REVERT: A4  469 GLU cc_start: 0.7174 (pt0) cc_final: 0.6908 (mt-10)
  outliers start: 37
  outliers final: 25
  residues processed: 198
  average time/residue: 0.7296
  time to fit residues: 170.2808
Evaluate side-chains
  200 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 167
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A1 residue   60 TYR
Chi-restraints excluded: chain A1 residue   83 VAL
Chi-restraints excluded: chain A1 residue  249 VAL
Chi-restraints excluded: chain A1 residue  275 SER
Chi-restraints excluded: chain A1 residue  343 ILE
Chi-restraints excluded: chain A1 residue  471 GLU
Chi-restraints excluded: chain A2 residue   60 TYR
Chi-restraints excluded: chain A2 residue   83 VAL
Chi-restraints excluded: chain A2 residue  139 VAL
Chi-restraints excluded: chain A2 residue  248 SER
Chi-restraints excluded: chain A2 residue  275 SER
Chi-restraints excluded: chain A2 residue  330 CYS
Chi-restraints excluded: chain A2 residue  343 ILE
Chi-restraints excluded: chain A3 residue   60 TYR
Chi-restraints excluded: chain A3 residue   83 VAL
Chi-restraints excluded: chain A3 residue  130 ILE
Chi-restraints excluded: chain A3 residue  139 VAL
Chi-restraints excluded: chain A3 residue  275 SER
Chi-restraints excluded: chain A3 residue  297 CYS
Chi-restraints excluded: chain A3 residue  311 GLU
Chi-restraints excluded: chain A3 residue  343 ILE
Chi-restraints excluded: chain A3 residue  402 ARG
Chi-restraints excluded: chain A4 residue   60 TYR
Chi-restraints excluded: chain A4 residue   83 VAL
Chi-restraints excluded: chain A4 residue  139 VAL
Chi-restraints excluded: chain A4 residue  151 SER
Chi-restraints excluded: chain A4 residue  173 SER
Chi-restraints excluded: chain A4 residue  248 SER
Chi-restraints excluded: chain A4 residue  275 SER
Chi-restraints excluded: chain A4 residue  311 GLU
Chi-restraints excluded: chain A4 residue  343 ILE
Chi-restraints excluded: chain A4 residue  402 ARG
Chi-restraints excluded: chain A4 residue  461 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 115 optimal weight:    0.5980
   chunk 165 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9990
   chunk 144 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.3188

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

Flipped N/Q/H residues before XYZ refinement:
** A1 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3 346 ASN
** A4 251 ASN ** 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 = 0.4177 r_free = 0.4177 target = 0.193065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.161022 restraints weight = 44368.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3874 rms_B_bonded: 1.78
r_work: 0.3789 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3688 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.5377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  15636  Z= 0.142
  Angle     :  0.492   5.402  21216  Z= 0.274
  Chirality :  0.038   0.139   2376
  Planarity :  0.004   0.045   2636
  Dihedral  :  4.889  47.335   2023
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.75 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.19), residues: 1824
  helix:  1.94 (0.15), residues: 1048
  sheet: -0.21 (0.36), residues: 184
  loop : -0.60 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARGA4 475 
 TYR   0.023   0.002   TYRA1  68 
 PHE   0.019   0.001   PHEA4 421 
 TRP   0.008   0.001   TRPA3 114 
 HIS   0.004   0.002   HISA1 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (15632)
  covalent geometry    : angle       0.49205 (21208)
  SS BOND              : bond        0.00161 (    4)
  SS BOND              : angle       0.43981 (    8)
  hydrogen bonds       : bond        0.04453 (  913)
  hydrogen bonds       : angle       4.33337 ( 2652)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 167
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A1   60 TYR cc_start: 0.4408 (OUTLIER) cc_final: 0.2690 (t80)
REVERT: A1  163 LYS cc_start: 0.5968 (mttt) cc_final: 0.4970 (mmmt)
REVERT: A1  471 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7317 (tt0)
REVERT: A1  498 LEU cc_start: 0.7956 (tt) cc_final: 0.7696 (mp)
REVERT: A2   60 TYR cc_start: 0.4307 (OUTLIER) cc_final: 0.2698 (t80)
REVERT: A2  502 ASN cc_start: 0.7687 (t0) cc_final: 0.7193 (m110)
REVERT: A3   60 TYR cc_start: 0.4221 (OUTLIER) cc_final: 0.2689 (t80)
REVERT: A3  163 LYS cc_start: 0.5979 (mttt) cc_final: 0.4867 (mmmt)
REVERT: A3  402 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6708 (mtm-85)
REVERT: A4   60 TYR cc_start: 0.4274 (OUTLIER) cc_final: 0.2703 (t80)
REVERT: A4  163 LYS cc_start: 0.5948 (mttt) cc_final: 0.4871 (mmmt)
REVERT: A4  402 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6793 (mtm-85)
REVERT: A4  469 GLU cc_start: 0.7161 (pt0) cc_final: 0.6882 (mt-10)
  outliers start: 37
  outliers final: 29
  residues processed: 200
  average time/residue: 0.6696
  time to fit residues: 159.4542
Evaluate side-chains
  201 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 165
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A1 residue   60 TYR
Chi-restraints excluded: chain A1 residue   83 VAL
Chi-restraints excluded: chain A1 residue  134 ASN
Chi-restraints excluded: chain A1 residue  275 SER
Chi-restraints excluded: chain A1 residue  343 ILE
Chi-restraints excluded: chain A1 residue  471 GLU
Chi-restraints excluded: chain A2 residue   60 TYR
Chi-restraints excluded: chain A2 residue   83 VAL
Chi-restraints excluded: chain A2 residue  139 VAL
Chi-restraints excluded: chain A2 residue  248 SER
Chi-restraints excluded: chain A2 residue  275 SER
Chi-restraints excluded: chain A2 residue  297 CYS
Chi-restraints excluded: chain A2 residue  330 CYS
Chi-restraints excluded: chain A2 residue  343 ILE
Chi-restraints excluded: chain A3 residue   60 TYR
Chi-restraints excluded: chain A3 residue   83 VAL
Chi-restraints excluded: chain A3 residue  130 ILE
Chi-restraints excluded: chain A3 residue  139 VAL
Chi-restraints excluded: chain A3 residue  248 SER
Chi-restraints excluded: chain A3 residue  275 SER
Chi-restraints excluded: chain A3 residue  297 CYS
Chi-restraints excluded: chain A3 residue  311 GLU
Chi-restraints excluded: chain A3 residue  343 ILE
Chi-restraints excluded: chain A3 residue  402 ARG
Chi-restraints excluded: chain A4 residue   60 TYR
Chi-restraints excluded: chain A4 residue   83 VAL
Chi-restraints excluded: chain A4 residue  134 ASN
Chi-restraints excluded: chain A4 residue  139 VAL
Chi-restraints excluded: chain A4 residue  151 SER
Chi-restraints excluded: chain A4 residue  173 SER
Chi-restraints excluded: chain A4 residue  248 SER
Chi-restraints excluded: chain A4 residue  275 SER
Chi-restraints excluded: chain A4 residue  311 GLU
Chi-restraints excluded: chain A4 residue  343 ILE
Chi-restraints excluded: chain A4 residue  402 ARG
Chi-restraints excluded: chain A4 residue  461 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 141 optimal weight:    2.9990
   chunk 173 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 124 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 149 optimal weight:    0.0770
   chunk 81 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.9542

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

Flipped N/Q/H residues before XYZ refinement:
** A1 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3 346 ASN
** A4 251 ASN ** 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 = 0.4190 r_free = 0.4190 target = 0.194460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.162544 restraints weight = 44464.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3891 rms_B_bonded: 1.77
r_work: 0.3807 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3705 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.5436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15636  Z= 0.121
  Angle     :  0.468   5.132  21216  Z= 0.260
  Chirality :  0.037   0.138   2376
  Planarity :  0.004   0.044   2636
  Dihedral  :  4.641  31.987   2022
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 16.99 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.46 (0.19), residues: 1824
  helix:  2.04 (0.15), residues: 1048
  sheet: -0.25 (0.36), residues: 184
  loop : -0.55 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARGA4 475 
 TYR   0.024   0.001   TYRA1  68 
 PHE   0.019   0.001   PHEA4 421 
 TRP   0.007   0.001   TRPA3 375 
 HIS   0.002   0.001   HISA1 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (15632)
  covalent geometry    : angle       0.46822 (21208)
  SS BOND              : bond        0.00139 (    4)
  SS BOND              : angle       0.48517 (    8)
  hydrogen bonds       : bond        0.04237 (  913)
  hydrogen bonds       : angle       4.24774 ( 2652)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9320.71 seconds
wall clock time: 158 minutes 30.92 seconds (9510.92 seconds total)