Starting phenix.real_space_refine
on Thu Jun 26 05:56:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dli_46979/06_2025/9dli_46979.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dli_46979/06_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_46979/06_2025/9dli_46979.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dli_46979/06_2025/9dli_46979.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dli_46979/06_2025/9dli_46979.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dli_46979/06_2025/9dli_46979.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.08s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 28.89, per 1000 atoms: 0.95
  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: 7.66
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  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: 2.55
  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: 12.43

  Time building geometry restraints manager: 9.43 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: 0.05
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:             1059.380
  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:             0.470
  Extract box with map and model:          1.570
  Check model and map are aligned:         0.200
  Set scattering table:                    0.240
  Process input model:                     80.930
  Find NCS groups from input model:        0.970
  Set up NCS constraints:                  0.120
  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:15.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total: 1158.950
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (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
 TRP   0.116   0.022   TRPA4 276 
 HIS   0.008   0.004   HISA4 371 
 PHE   0.084   0.012   PHEA2 421 
 TYR   0.151   0.022   TYRA3  68 
 ARG   0.012   0.002   ARGA3 146 

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

*********************** 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  : 2.374 
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
  outliers start: 6
  outliers final: 9
  residues processed: 335
  average time/residue: 2.1191
  time to fit residues: 805.8935
Evaluate side-chains
  203 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 194
  time to evaluate  : 2.231 
-------------------------------------------------------------------------------
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 155 optimal weight:    0.9990
   chunk 139 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 94 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 144 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9980
   chunk 107 optimal weight:    1.9990
   chunk 167 optimal weight:    5.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A1 457 GLN
A1 495 ASN
A1 502 ASN
A2 457 GLN
A2 495 ASN
A3 399 ASN
A3 457 GLN
A4 457 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.202498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.170515 restraints weight = 44070.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3961 rms_B_bonded: 1.82
r_work: 0.3876 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3770 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.3202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  15636  Z= 0.150
  Angle     :  0.568   5.757  21216  Z= 0.323
  Chirality :  0.040   0.153   2376
  Planarity :  0.004   0.037   2636
  Dihedral  :  5.791  33.394   2037
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.42 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.19), residues: 1824
  helix:  1.33 (0.15), residues: 1040
  sheet:  0.20 (0.37), residues: 184
  loop : -0.48 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRPA4 235 
 HIS   0.003   0.001   HISA4 200 
 PHE   0.027   0.002   PHEA2 421 
 TYR   0.024   0.002   TYRA3  68 
 ARG   0.003   0.000   ARGA4 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05357 (  913)
  hydrogen bonds       : angle       4.60140 ( 2652)
  SS BOND              : bond        0.00160 (    4)
  SS BOND              : angle       0.51641 (    8)
  covalent geometry    : bond        0.00308 (15632)
  covalent geometry    : angle       0.56808 (21208)

*********************** 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
  259 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 230
  time to evaluate  : 2.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A1  330 CYS cc_start: 0.7779 (t) cc_final: 0.7361 (p)
REVERT: A2  330 CYS cc_start: 0.7840 (t) cc_final: 0.7559 (p)
REVERT: A2  386 THR cc_start: 0.6922 (p) cc_final: 0.6715 (m)
REVERT: A2  442 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8242 (t)
REVERT: A3  311 GLU cc_start: 0.5412 (OUTLIER) cc_final: 0.4743 (tt0)
REVERT: A3  330 CYS cc_start: 0.7726 (t) cc_final: 0.7464 (p)
REVERT: A4  292 PHE cc_start: 0.6391 (m-80) cc_final: 0.6154 (m-80)
REVERT: A4  330 CYS cc_start: 0.7756 (t) cc_final: 0.7376 (p)
  outliers start: 29
  outliers final: 14
  residues processed: 253
  average time/residue: 1.8290
  time to fit residues: 536.8269
Evaluate side-chains
  185 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 169
  time to evaluate  : 2.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A1 residue  248 SER
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 34 optimal weight:    7.9990
   chunk 102 optimal weight:    1.9990
   chunk 173 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9990
   chunk 104 optimal weight:    2.9990
   chunk 162 optimal weight:    6.9990
   chunk 183 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 111 optimal weight:    0.8980
   chunk 42 optimal weight:    0.6980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A1 399 ASN
A2 399 ASN
A3 352 ASN
A3 399 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.196891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.163850 restraints weight = 44444.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.3890 rms_B_bonded: 1.83
r_work: 0.3803 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3697 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.4043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15636  Z= 0.157
  Angle     :  0.535   5.102  21216  Z= 0.303
  Chirality :  0.039   0.141   2376
  Planarity :  0.005   0.044   2636
  Dihedral  :  5.304  34.280   2030
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 13.16 %
    Favored  : 84.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.19), residues: 1824
  helix:  1.69 (0.15), residues: 1044
  sheet: -0.17 (0.37), residues: 184
  loop : -0.49 (0.26), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRPA2 375 
 HIS   0.004   0.002   HISA4 200 
 PHE   0.022   0.002   PHEA2 421 
 TYR   0.026   0.002   TYRA4  68 
 ARG   0.003   0.001   ARGA2 285 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05016 (  913)
  hydrogen bonds       : angle       4.50535 ( 2652)
  SS BOND              : bond        0.00214 (    4)
  SS BOND              : angle       0.52290 (    8)
  covalent geometry    : bond        0.00349 (15632)
  covalent geometry    : angle       0.53473 (21208)

*********************** 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
  230 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 187
  time to evaluate  : 2.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A1   60 TYR cc_start: 0.4092 (OUTLIER) cc_final: 0.3515 (t80)
REVERT: A1  330 CYS cc_start: 0.7743 (t) cc_final: 0.7349 (p)
REVERT: A1  472 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7149 (tp30)
REVERT: A2  330 CYS cc_start: 0.7709 (t) cc_final: 0.7485 (p)
REVERT: A2  386 THR cc_start: 0.7014 (p) cc_final: 0.6809 (m)
REVERT: A2  502 ASN cc_start: 0.7659 (t0) cc_final: 0.6960 (m110)
REVERT: A3  311 GLU cc_start: 0.5214 (OUTLIER) cc_final: 0.3734 (mp0)
REVERT: A3  330 CYS cc_start: 0.7709 (t) cc_final: 0.7461 (p)
REVERT: A3  472 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7280 (tp30)
REVERT: A4  330 CYS cc_start: 0.7746 (t) cc_final: 0.7460 (p)
REVERT: A4  386 THR cc_start: 0.7072 (p) cc_final: 0.6864 (m)
  outliers start: 43
  outliers final: 26
  residues processed: 222
  average time/residue: 1.6289
  time to fit residues: 428.5690
Evaluate side-chains
  185 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 155
  time to evaluate  : 2.093 
-------------------------------------------------------------------------------
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  275 SER
Chi-restraints excluded: chain A1 residue  343 ILE
Chi-restraints excluded: chain A1 residue  461 ILE
Chi-restraints excluded: chain A1 residue  472 GLU
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  130 ILE
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  418 LEU
Chi-restraints excluded: chain A3 residue  461 ILE
Chi-restraints excluded: chain A3 residue  472 GLU
Chi-restraints excluded: chain A4 residue  248 SER
Chi-restraints excluded: chain A4 residue  275 SER
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 161 optimal weight:    0.7980
   chunk 70 optimal weight:    8.9990
   chunk 47 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 27 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 126 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 123 optimal weight:    4.9990
   overall best weight:    2.5588

-------------------------------------------------------------------------------
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 502 ASN
** A2 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3 352 ASN
A3 399 ASN
A3 502 ASN
** A4 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A4 502 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.192892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.160449 restraints weight = 44774.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3875 rms_B_bonded: 1.80
r_work: 0.3792 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3694 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.4582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  15636  Z= 0.229
  Angle     :  0.602   5.472  21216  Z= 0.338
  Chirality :  0.042   0.142   2376
  Planarity :  0.005   0.046   2636
  Dihedral  :  5.562  35.162   2030
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 13.04 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.19), residues: 1824
  helix:  1.46 (0.15), residues: 1048
  sheet: -0.03 (0.38), residues: 184
  loop : -0.67 (0.26), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRPA2 187 
 HIS   0.007   0.003   HISA2 200 
 PHE   0.023   0.002   PHEA2 421 
 TYR   0.027   0.002   TYRA3  68 
 ARG   0.004   0.001   ARGA1 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05405 (  913)
  hydrogen bonds       : angle       4.67581 ( 2652)
  SS BOND              : bond        0.00243 (    4)
  SS BOND              : angle       0.43839 (    8)
  covalent geometry    : bond        0.00536 (15632)
  covalent geometry    : angle       0.60255 (21208)

*********************** 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
  238 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 176
  time to evaluate  : 2.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A1   60 TYR cc_start: 0.4497 (OUTLIER) cc_final: 0.2870 (t80)
REVERT: A1  330 CYS cc_start: 0.7701 (t) cc_final: 0.7394 (p)
REVERT: A1  471 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7418 (tt0)
REVERT: A2   60 TYR cc_start: 0.4254 (OUTLIER) cc_final: 0.2758 (t80)
REVERT: A2  333 VAL cc_start: 0.7756 (OUTLIER) cc_final: 0.7506 (t)
REVERT: A3   60 TYR cc_start: 0.4326 (OUTLIER) cc_final: 0.2818 (t80)
REVERT: A4   60 TYR cc_start: 0.4191 (OUTLIER) cc_final: 0.2778 (t80)
REVERT: A4  330 CYS cc_start: 0.7732 (t) cc_final: 0.7519 (p)
REVERT: A4  386 THR cc_start: 0.7165 (p) cc_final: 0.6946 (m)
  outliers start: 62
  outliers final: 36
  residues processed: 224
  average time/residue: 1.5260
  time to fit residues: 408.2296
Evaluate side-chains
  205 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 163
  time to evaluate  : 2.117 
-------------------------------------------------------------------------------
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  190 THR
Chi-restraints excluded: chain A1 residue  248 SER
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  134 ASN
Chi-restraints excluded: chain A2 residue  139 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  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  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  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  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 175 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 177 optimal weight:    0.9980
   chunk 121 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 87 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 17 optimal weight:    0.3980
   chunk 148 optimal weight:    1.9990
   chunk 115 optimal weight:    1.9990
   chunk 181 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A1 399 ASN
A2 399 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 = 0.4208 r_free = 0.4208 target = 0.196345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.163729 restraints weight = 44026.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 1.79
r_work: 0.3814 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3711 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.4824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  15636  Z= 0.115
  Angle     :  0.471   4.313  21216  Z= 0.263
  Chirality :  0.037   0.139   2376
  Planarity :  0.004   0.045   2636
  Dihedral  :  4.981  32.033   2030
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.17 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.19), residues: 1824
  helix:  1.84 (0.15), residues: 1048
  sheet: -0.28 (0.38), residues: 184
  loop : -0.46 (0.26), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRPA2 375 
 HIS   0.002   0.001   HISA2 200 
 PHE   0.020   0.001   PHEA4 421 
 TYR   0.015   0.001   TYRA1  48 
 ARG   0.002   0.000   ARGA4 475 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04366 (  913)
  hydrogen bonds       : angle       4.30973 ( 2652)
  SS BOND              : bond        0.00156 (    4)
  SS BOND              : angle       0.44875 (    8)
  covalent geometry    : bond        0.00242 (15632)
  covalent geometry    : angle       0.47073 (21208)

*********************** 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
  213 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 176
  time to evaluate  : 2.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A1   60 TYR cc_start: 0.4336 (OUTLIER) cc_final: 0.2677 (t80)
REVERT: A1  330 CYS cc_start: 0.7702 (t) cc_final: 0.7381 (p)
REVERT: A1  471 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7273 (tt0)
REVERT: A1  498 LEU cc_start: 0.8041 (tt) cc_final: 0.7627 (mp)
REVERT: A2   60 TYR cc_start: 0.4129 (OUTLIER) cc_final: 0.2660 (t80)
REVERT: A2  502 ASN cc_start: 0.7602 (t0) cc_final: 0.7123 (m110)
REVERT: A3   60 TYR cc_start: 0.4121 (OUTLIER) cc_final: 0.2689 (t80)
REVERT: A4   60 TYR cc_start: 0.4017 (OUTLIER) cc_final: 0.2646 (t80)
REVERT: A4   68 TYR cc_start: 0.7666 (t80) cc_final: 0.7450 (t80)
REVERT: A4  130 ILE cc_start: 0.5984 (OUTLIER) cc_final: 0.5776 (mt)
REVERT: A4  330 CYS cc_start: 0.7726 (t) cc_final: 0.7503 (p)
REVERT: A4  386 THR cc_start: 0.7123 (p) cc_final: 0.6901 (m)
  outliers start: 37
  outliers final: 23
  residues processed: 208
  average time/residue: 1.4602
  time to fit residues: 364.2354
Evaluate side-chains
  190 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 161
  time to evaluate  : 2.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A1 residue   60 TYR
Chi-restraints excluded: chain A1 residue  139 VAL
Chi-restraints excluded: chain A1 residue  190 THR
Chi-restraints excluded: chain A1 residue  248 SER
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  343 ILE
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  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  461 ILE
Chi-restraints excluded: chain A4 residue   60 TYR
Chi-restraints excluded: chain A4 residue  130 ILE
Chi-restraints excluded: chain A4 residue  248 SER
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 113 optimal weight:    2.9990
   chunk 173 optimal weight:    1.9990
   chunk 133 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   chunk 72 optimal weight:    5.9990
   chunk 91 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 87 optimal weight:    2.9990
   chunk 127 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   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**
** A4 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.190607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.158019 restraints weight = 44895.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3839 rms_B_bonded: 1.80
r_work: 0.3752 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3649 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.5039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070  15636  Z= 0.244
  Angle     :  0.597   5.612  21216  Z= 0.335
  Chirality :  0.042   0.142   2376
  Planarity :  0.005   0.050   2636
  Dihedral  :  5.449  34.899   2030
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 14.00 %
    Favored  : 82.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.19), residues: 1824
  helix:  1.56 (0.15), residues: 1048
  sheet: -0.07 (0.38), residues: 184
  loop : -0.67 (0.26), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRPA1 187 
 HIS   0.007   0.003   HISA2 200 
 PHE   0.022   0.002   PHEA2 421 
 TYR   0.017   0.002   TYRA1  48 
 ARG   0.004   0.001   ARGA1 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05351 (  913)
  hydrogen bonds       : angle       4.66540 ( 2652)
  SS BOND              : bond        0.00267 (    4)
  SS BOND              : angle       0.32933 (    8)
  covalent geometry    : bond        0.00578 (15632)
  covalent geometry    : angle       0.59667 (21208)

*********************** 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
  235 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 174
  time to evaluate  : 2.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A1   60 TYR cc_start: 0.4498 (OUTLIER) cc_final: 0.2812 (t80)
REVERT: A1   85 LYS cc_start: 0.7187 (pmmt) cc_final: 0.6504 (mmtm)
REVERT: A1  330 CYS cc_start: 0.7668 (t) cc_final: 0.7376 (p)
REVERT: A1  471 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7418 (tt0)
REVERT: A2   60 TYR cc_start: 0.4316 (OUTLIER) cc_final: 0.2721 (t80)
REVERT: A3   60 TYR cc_start: 0.4283 (OUTLIER) cc_final: 0.2749 (t80)
REVERT: A4   60 TYR cc_start: 0.4311 (OUTLIER) cc_final: 0.2768 (t80)
REVERT: A4  163 LYS cc_start: 0.6035 (mttt) cc_final: 0.4977 (mmmt)
REVERT: A4  330 CYS cc_start: 0.7632 (t) cc_final: 0.7426 (p)
REVERT: A4  386 THR cc_start: 0.7147 (p) cc_final: 0.6917 (m)
  outliers start: 61
  outliers final: 41
  residues processed: 224
  average time/residue: 1.4742
  time to fit residues: 396.2340
Evaluate side-chains
  215 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 169
  time to evaluate  : 2.228 
-------------------------------------------------------------------------------
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  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  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  139 VAL
Chi-restraints excluded: chain A2 residue  171 VAL
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  330 CYS
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  461 ILE
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  171 VAL
Chi-restraints excluded: chain A4 residue  173 SER
Chi-restraints excluded: chain A4 residue  248 SER
Chi-restraints excluded: chain A4 residue  249 VAL
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 175 optimal weight:    2.9990
   chunk 129 optimal weight:    2.9990
   chunk 93 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   chunk 165 optimal weight:    3.9990
   chunk 120 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 108 optimal weight:    3.9990
   chunk 46 optimal weight:   10.0000
   chunk 160 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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 502 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 = 0.4180 r_free = 0.4180 target = 0.193267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.160933 restraints weight = 44532.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3877 rms_B_bonded: 1.79
r_work: 0.3791 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3691 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.5138

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= 0.145
  Angle     :  0.498   4.445  21216  Z= 0.278
  Chirality :  0.038   0.139   2376
  Planarity :  0.005   0.049   2636
  Dihedral  :  5.006  32.115   2026
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 15.13 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.19), residues: 1824
  helix:  1.82 (0.15), residues: 1048
  sheet: -0.23 (0.37), residues: 184
  loop : -0.55 (0.26), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRPA3 375 
 HIS   0.004   0.002   HISA3 200 
 PHE   0.020   0.001   PHEA4 421 
 TYR   0.017   0.002   TYRA1  48 
 ARG   0.003   0.000   ARGA3 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04611 (  913)
  hydrogen bonds       : angle       4.39524 ( 2652)
  SS BOND              : bond        0.00204 (    4)
  SS BOND              : angle       0.44891 (    8)
  covalent geometry    : bond        0.00323 (15632)
  covalent geometry    : angle       0.49760 (21208)

*********************** 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
  220 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 174
  time to evaluate  : 2.552 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A1   60 TYR cc_start: 0.4482 (OUTLIER) cc_final: 0.2780 (t80)
REVERT: A1  330 CYS cc_start: 0.7748 (t) cc_final: 0.7503 (p)
REVERT: A1  471 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7331 (tt0)
REVERT: A1  498 LEU cc_start: 0.8036 (tt) cc_final: 0.7721 (mp)
REVERT: A2   60 TYR cc_start: 0.4292 (OUTLIER) cc_final: 0.2717 (t80)
REVERT: A2  502 ASN cc_start: 0.7730 (t0) cc_final: 0.7219 (m110)
REVERT: A3   60 TYR cc_start: 0.4259 (OUTLIER) cc_final: 0.2754 (t80)
REVERT: A4   60 TYR cc_start: 0.4296 (OUTLIER) cc_final: 0.2775 (t80)
REVERT: A4  163 LYS cc_start: 0.6015 (mttt) cc_final: 0.4947 (mmmt)
REVERT: A4  311 GLU cc_start: 0.5061 (OUTLIER) cc_final: 0.3174 (mp0)
REVERT: A4  386 THR cc_start: 0.7166 (p) cc_final: 0.6949 (m)
  outliers start: 46
  outliers final: 31
  residues processed: 215
  average time/residue: 1.8009
  time to fit residues: 471.8076
Evaluate side-chains
  202 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 165
  time to evaluate  : 2.164 
-------------------------------------------------------------------------------
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  190 THR
Chi-restraints excluded: chain A1 residue  248 SER
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  139 VAL
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  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  139 VAL
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  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  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  461 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 156 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 150 optimal weight:    2.9990
   chunk 138 optimal weight:   10.0000
   chunk 154 optimal weight:    2.9990
   chunk 119 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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**
** A4 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.191791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.159273 restraints weight = 44654.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3853 rms_B_bonded: 1.78
r_work: 0.3767 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3665 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.5225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  15636  Z= 0.186
  Angle     :  0.538   4.892  21216  Z= 0.301
  Chirality :  0.040   0.141   2376
  Planarity :  0.005   0.050   2636
  Dihedral  :  5.128  34.434   2026
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 14.89 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.19), residues: 1824
  helix:  1.76 (0.15), residues: 1048
  sheet: -0.17 (0.37), residues: 184
  loop : -0.61 (0.26), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRPA3 114 
 HIS   0.005   0.003   HISA1 200 
 PHE   0.020   0.002   PHEA4 421 
 TYR   0.017   0.002   TYRA1  48 
 ARG   0.005   0.000   ARGA2 475 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04890 (  913)
  hydrogen bonds       : angle       4.49418 ( 2652)
  SS BOND              : bond        0.00201 (    4)
  SS BOND              : angle       0.33428 (    8)
  covalent geometry    : bond        0.00432 (15632)
  covalent geometry    : angle       0.53779 (21208)

*********************** 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
  222 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 172
  time to evaluate  : 2.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A1   60 TYR cc_start: 0.4483 (OUTLIER) cc_final: 0.2778 (t80)
REVERT: A1  330 CYS cc_start: 0.7695 (t) cc_final: 0.7465 (p)
REVERT: A1  471 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7359 (tt0)
REVERT: A1  498 LEU cc_start: 0.8020 (tt) cc_final: 0.7714 (mp)
REVERT: A2   60 TYR cc_start: 0.4348 (OUTLIER) cc_final: 0.2704 (t80)
REVERT: A2  502 ASN cc_start: 0.7755 (t0) cc_final: 0.7164 (m110)
REVERT: A3   60 TYR cc_start: 0.4316 (OUTLIER) cc_final: 0.2758 (t80)
REVERT: A3  281 LEU cc_start: 0.5841 (OUTLIER) cc_final: 0.5427 (mt)
REVERT: A4   60 TYR cc_start: 0.4337 (OUTLIER) cc_final: 0.2755 (t80)
REVERT: A4  163 LYS cc_start: 0.5996 (mttt) cc_final: 0.4937 (mmmt)
REVERT: A4  386 THR cc_start: 0.7113 (p) cc_final: 0.6901 (m)
  outliers start: 50
  outliers final: 38
  residues processed: 210
  average time/residue: 1.3813
  time to fit residues: 351.0665
Evaluate side-chains
  212 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 168
  time to evaluate  : 2.297 
-------------------------------------------------------------------------------
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  190 THR
Chi-restraints excluded: chain A1 residue  248 SER
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  134 ASN
Chi-restraints excluded: chain A2 residue  139 VAL
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  330 CYS
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  130 ILE
Chi-restraints excluded: chain A3 residue  134 ASN
Chi-restraints excluded: chain A3 residue  139 VAL
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  297 CYS
Chi-restraints excluded: chain A3 residue  311 GLU
Chi-restraints excluded: chain A3 residue  343 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  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  311 GLU
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 96 optimal weight:    1.9990
   chunk 177 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 94 optimal weight:    8.9990
   chunk 142 optimal weight:    0.9990
   chunk 136 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 72 optimal weight:    0.4980
   chunk 159 optimal weight:    2.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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 = 0.4182 r_free = 0.4182 target = 0.193495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.161179 restraints weight = 44483.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3877 rms_B_bonded: 1.79
r_work: 0.3793 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3692 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.5295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  15636  Z= 0.140
  Angle     :  0.489   4.520  21216  Z= 0.273
  Chirality :  0.038   0.139   2376
  Planarity :  0.004   0.048   2636
  Dihedral  :  4.869  32.589   2024
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 15.67 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.19), residues: 1824
  helix:  1.93 (0.15), residues: 1048
  sheet: -0.25 (0.37), residues: 184
  loop : -0.57 (0.26), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRPA3 114 
 HIS   0.003   0.002   HISA2 200 
 PHE   0.019   0.001   PHEA4 421 
 TYR   0.016   0.002   TYRA1  48 
 ARG   0.004   0.000   ARGA2 475 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04502 (  913)
  hydrogen bonds       : angle       4.34692 ( 2652)
  SS BOND              : bond        0.00181 (    4)
  SS BOND              : angle       0.41420 (    8)
  covalent geometry    : bond        0.00311 (15632)
  covalent geometry    : angle       0.48895 (21208)

*********************** 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
  210 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 170
  time to evaluate  : 2.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A1   60 TYR cc_start: 0.4441 (OUTLIER) cc_final: 0.2720 (t80)
REVERT: A1  330 CYS cc_start: 0.7708 (t) cc_final: 0.7483 (p)
REVERT: A1  471 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7300 (tt0)
REVERT: A1  498 LEU cc_start: 0.7955 (tt) cc_final: 0.7689 (mp)
REVERT: A2   60 TYR cc_start: 0.4265 (OUTLIER) cc_final: 0.2677 (t80)
REVERT: A2   68 TYR cc_start: 0.7634 (t80) cc_final: 0.7374 (t80)
REVERT: A2  502 ASN cc_start: 0.7674 (t0) cc_final: 0.7176 (m110)
REVERT: A3   60 TYR cc_start: 0.4244 (OUTLIER) cc_final: 0.2722 (t80)
REVERT: A4   60 TYR cc_start: 0.4295 (OUTLIER) cc_final: 0.2740 (t80)
REVERT: A4   72 ARG cc_start: 0.7511 (ttt180) cc_final: 0.7140 (ttp80)
REVERT: A4  163 LYS cc_start: 0.5991 (mttt) cc_final: 0.4914 (mmmt)
REVERT: A4  386 THR cc_start: 0.7117 (p) cc_final: 0.6909 (m)
  outliers start: 40
  outliers final: 34
  residues processed: 205
  average time/residue: 1.4027
  time to fit residues: 348.7101
Evaluate side-chains
  207 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 168
  time to evaluate  : 2.179 
-------------------------------------------------------------------------------
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  190 THR
Chi-restraints excluded: chain A1 residue  248 SER
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  134 ASN
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 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  139 VAL
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  297 CYS
Chi-restraints excluded: chain A3 residue  311 GLU
Chi-restraints excluded: chain A3 residue  343 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  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  461 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 152 optimal weight:    0.4980
   chunk 73 optimal weight:    6.9990
   chunk 149 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   chunk 140 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 163 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9980
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 = 0.4184 r_free = 0.4184 target = 0.193700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.161452 restraints weight = 44477.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3880 rms_B_bonded: 1.79
r_work: 0.3795 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3693 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.5332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  15636  Z= 0.138
  Angle     :  0.486   4.511  21216  Z= 0.271
  Chirality :  0.038   0.139   2376
  Planarity :  0.004   0.048   2636
  Dihedral  :  4.828  32.081   2024
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 15.61 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.19), residues: 1824
  helix:  1.97 (0.15), residues: 1048
  sheet: -0.26 (0.37), residues: 184
  loop : -0.57 (0.26), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRPA3 114 
 HIS   0.003   0.002   HISA1 200 
 PHE   0.019   0.001   PHEA4 421 
 TYR   0.017   0.002   TYRA1  48 
 ARG   0.004   0.000   ARGA2 475 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04443 (  913)
  hydrogen bonds       : angle       4.32219 ( 2652)
  SS BOND              : bond        0.00145 (    4)
  SS BOND              : angle       0.36716 (    8)
  covalent geometry    : bond        0.00309 (15632)
  covalent geometry    : angle       0.48579 (21208)

********************** 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
  214 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 172
  time to evaluate  : 2.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A1   60 TYR cc_start: 0.4416 (OUTLIER) cc_final: 0.2680 (t80)
REVERT: A1  330 CYS cc_start: 0.7695 (t) cc_final: 0.7471 (p)
REVERT: A1  471 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7306 (tt0)
REVERT: A1  498 LEU cc_start: 0.7929 (tt) cc_final: 0.7673 (mp)
REVERT: A2   60 TYR cc_start: 0.4292 (OUTLIER) cc_final: 0.2691 (t80)
REVERT: A2   68 TYR cc_start: 0.7662 (t80) cc_final: 0.7380 (t80)
REVERT: A2  502 ASN cc_start: 0.7670 (t0) cc_final: 0.7177 (m110)
REVERT: A3   60 TYR cc_start: 0.4221 (OUTLIER) cc_final: 0.2705 (t80)
REVERT: A4   60 TYR cc_start: 0.4281 (OUTLIER) cc_final: 0.2718 (t80)
REVERT: A4   72 ARG cc_start: 0.7520 (ttt180) cc_final: 0.7153 (ttp80)
REVERT: A4  163 LYS cc_start: 0.5989 (mttt) cc_final: 0.4912 (mmmt)
REVERT: A4  386 THR cc_start: 0.7092 (p) cc_final: 0.6891 (m)
  outliers start: 42
  outliers final: 37
  residues processed: 208
  average time/residue: 1.4955
  time to fit residues: 379.6634
Evaluate side-chains
  211 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 169
  time to evaluate  : 2.099 
-------------------------------------------------------------------------------
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  190 THR
Chi-restraints excluded: chain A1 residue  248 SER
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  134 ASN
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 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  139 VAL
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  297 CYS
Chi-restraints excluded: chain A3 residue  311 GLU
Chi-restraints excluded: chain A3 residue  343 ILE
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  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  461 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 55 optimal weight:    0.6980
   chunk 100 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 180 optimal weight:    0.6980
   chunk 108 optimal weight:    4.9990
   chunk 93 optimal weight:    4.9990
   chunk 158 optimal weight:    1.9990
   chunk 156 optimal weight:    2.9990
   chunk 181 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.4195 r_free = 0.4195 target = 0.194926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.162874 restraints weight = 44226.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3893 rms_B_bonded: 1.78
r_work: 0.3809 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3706 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.5374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15636  Z= 0.122
  Angle     :  0.465   4.487  21216  Z= 0.259
  Chirality :  0.037   0.138   2376
  Planarity :  0.004   0.047   2636
  Dihedral  :  4.697  31.562   2024
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.03 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.20), residues: 1824
  helix:  2.07 (0.15), residues: 1048
  sheet: -0.29 (0.37), residues: 184
  loop : -0.51 (0.26), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRPA3 114 
 HIS   0.003   0.001   HISA3 200 
 PHE   0.019   0.001   PHEA4 421 
 TYR   0.015   0.001   TYRA1  48 
 ARG   0.004   0.000   ARGA2 475 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04241 (  913)
  hydrogen bonds       : angle       4.24254 ( 2652)
  SS BOND              : bond        0.00127 (    4)
  SS BOND              : angle       0.41206 (    8)
  covalent geometry    : bond        0.00268 (15632)
  covalent geometry    : angle       0.46509 (21208)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 24262.13 seconds
wall clock time: 424 minutes 59.81 seconds (25499.81 seconds total)