Starting phenix.real_space_refine
on Tue Jul 29 04:09:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ou9_20198/07_2025/6ou9_20198.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ou9_20198/07_2025/6ou9_20198.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ou9_20198/07_2025/6ou9_20198.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ou9_20198/07_2025/6ou9_20198.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ou9_20198/07_2025/6ou9_20198.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ou9_20198/07_2025/6ou9_20198.cif"
  }
  resolution = 3.2
  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=   0.005 sd=   0.086
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    7211      2.51       5
     N    1916      2.21       5
     O    2085      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11269
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 3865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 507, 3865
          Classifications: {'peptide': 507}
          Link IDs: {'PTRANS': 51, 'TRANS': 455}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 3703
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 483, 3703
          Classifications: {'peptide': 483}
          Link IDs: {'PTRANS': 49, 'TRANS': 433}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 3701
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 483, 3701
          Classifications: {'peptide': 483}
          Link IDs: {'PTRANS': 49, 'TRANS': 433}
          Chain breaks: 2
  Time building chain proxies: 7.01, per 1000 atoms: 0.62
  Number of scatterers: 11269
  At special positions: 0
  Unit cell: (102.72, 109.14, 111.28, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      57     16.00
     O    2085      8.00
     N    1916      7.00
     C    7211      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.57
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2914 Ramachandran restraints generated.
    1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2710

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 19 sheets defined
      8.5% alpha, 25.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.24
  Creating SS restraints...
    Processing helix  chain 'B' and resid 42 through 46
      removed outlier: 3.957A  pdb=" N   ALA B  45 " --> pdb=" O   ALA B  42 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   ALA B  46 " --> pdb=" O   THR B  43 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 42 through 46'
    Processing helix  chain 'B' and resid 88 through 91
      removed outlier: 3.961A  pdb=" N   LEU B  91 " --> pdb=" O   GLY B  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 88 through 91'
    Processing helix  chain 'B' and resid 92 through 100
      removed outlier: 3.682A  pdb=" N   GLN B 100 " --> pdb=" O   GLN B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 146
      removed outlier: 3.555A  pdb=" N   THR B 145 " --> pdb=" O   GLY B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 242
    Processing helix  chain 'B' and resid 448 through 459
      removed outlier: 3.581A  pdb=" N   HIS B 454 " --> pdb=" O   GLU B 450 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   GLU B 457 " --> pdb=" O   SER B 453 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLN B 459 " --> pdb=" O   PHE B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 504
      removed outlier: 3.822A  pdb=" N   ASN B 503 " --> pdb=" O   GLY B 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 91
      removed outlier: 3.955A  pdb=" N   LEU A  91 " --> pdb=" O   GLY A  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 88 through 91'
    Processing helix  chain 'A' and resid 92 through 99
      removed outlier: 3.586A  pdb=" N   HIS A  97 " --> pdb=" O   PRO A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 147
      removed outlier: 3.778A  pdb=" N   PHE A 147 " --> pdb=" O   ALA A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 242
    Processing helix  chain 'A' and resid 448 through 459
      removed outlier: 3.577A  pdb=" N   GLU A 457 " --> pdb=" O   SER A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 504
      removed outlier: 3.692A  pdb=" N   ASN A 503 " --> pdb=" O   GLY A 500 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LEU A 504 " --> pdb=" O   PRO A 501 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 500 through 504'
    Processing helix  chain 'C' and resid 88 through 92
      removed outlier: 4.018A  pdb=" N   LEU C  91 " --> pdb=" O   GLY C  88 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ASN C  92 " --> pdb=" O   PRO C  89 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 88 through 92'
    Processing helix  chain 'C' and resid 94 through 99
    Processing helix  chain 'C' and resid 100 through 102
      No H-bonds generated for 'chain 'C' and resid 100 through 102'
    Processing helix  chain 'C' and resid 226 through 230
      removed outlier: 3.715A  pdb=" N   THR C 229 " --> pdb=" O   GLU C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 242
    Processing helix  chain 'C' and resid 448 through 459
      removed outlier: 3.529A  pdb=" N   VAL C 452 " --> pdb=" O   PRO C 448 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   HIS C 454 " --> pdb=" O   GLU C 450 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   GLU C 457 " --> pdb=" O   SER C 453 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 500 through 504
      removed outlier: 3.513A  pdb=" N   ASN C 503 " --> pdb=" O   GLY C 500 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 63 through 71
      removed outlier: 12.384A  pdb=" N   GLN B  64 " --> pdb=" O   PRO B 211 " (cutoff:3.500A)
      removed outlier: 10.354A  pdb=" N   THR B 209 " --> pdb=" O   PRO B  66 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   GLY B  68 " --> pdb=" O   VAL B 207 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ARG B 206 " --> pdb=" O   MET B 114 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU B 164 " --> pdb=" O   MET B 109 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 81 through 86
      removed outlier: 7.191A  pdb=" N   CYS B 185 " --> pdb=" O   LEU B  82 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   ASP B  84 " --> pdb=" O   LEU B 183 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   LEU B 183 " --> pdb=" O   ASP B  84 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   LYS B 124 " --> pdb=" O   TYR B 188 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   ALA B 122 " --> pdb=" O   PRO B 190 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 106
      removed outlier: 3.656A  pdb=" N   ASN B 216 " --> pdb=" O   VAL B 106 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 251 through 255
      removed outlier: 7.920A  pdb=" N   ILE B 251 " --> pdb=" O   ASP B 432 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   ASP B 432 " --> pdb=" O   ILE B 251 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   LYS B 253 " --> pdb=" O   MET B 430 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 290 through 296
      removed outlier: 4.238A  pdb=" N   LYS B 302 " --> pdb=" O   PHE B 369 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   GLU B 368 " --> pdb=" O   LYS B 355 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   LYS B 355 " --> pdb=" O   GLU B 368 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   ASP B 332 " --> pdb=" O   VAL B 386 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   VAL B 386 " --> pdb=" O   ASP B 332 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   HIS B 334 " --> pdb=" O   ALA B 384 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 425 through 426
      removed outlier: 3.960A  pdb=" N   PHE B 490 " --> pdb=" O   TYR B 486 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   ALA B 466 " --> pdb=" O   TRP B 515 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   TRP B 515 " --> pdb=" O   ALA B 466 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   LEU B 468 " --> pdb=" O   SER B 513 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 63 through 64
    Processing sheet with id=AA8, first strand: chain 'A' and resid 63 through 64
      removed outlier: 4.196A  pdb=" N   ALA A 204 " --> pdb=" O   ALA A 116 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 83 through 86
      removed outlier: 4.064A  pdb=" N   PHE A  83 " --> pdb=" O   CYS A 185 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 173 through 174
    Processing sheet with id=AB2, first strand: chain 'A' and resid 251 through 255
      removed outlier: 6.703A  pdb=" N   MET A 430 " --> pdb=" O   ASN A 252 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   MET A 254 " --> pdb=" O   TYR A 428 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   TYR A 428 " --> pdb=" O   MET A 254 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 349 through 354
      removed outlier: 3.700A  pdb=" N   TRP A 385 " --> pdb=" O   HIS A 334 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   SER A 336 " --> pdb=" O   LEU A 383 " (cutoff:3.500A)
      removed outlier: 5.746A  pdb=" N   LEU A 383 " --> pdb=" O   SER A 336 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   PHE A 338 " --> pdb=" O   GLY A 381 " (cutoff:3.500A)
      removed outlier: 5.319A  pdb=" N   GLY A 381 " --> pdb=" O   PHE A 338 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   LYS A 302 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   PHE A 369 " --> pdb=" O   LYS A 302 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 425 through 426
      removed outlier: 4.083A  pdb=" N   PHE A 490 " --> pdb=" O   TYR A 486 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   GLY A 481 " --> pdb=" O   TYR A 471 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ALA A 466 " --> pdb=" O   TRP A 515 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   TRP A 515 " --> pdb=" O   ALA A 466 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LEU A 468 " --> pdb=" O   SER A 513 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 63 through 72
      removed outlier: 12.388A  pdb=" N   GLN C  64 " --> pdb=" O   PRO C 211 " (cutoff:3.500A)
      removed outlier: 10.745A  pdb=" N   THR C 209 " --> pdb=" O   PRO C  66 " (cutoff:3.500A)
      removed outlier: 5.512A  pdb=" N   GLY C  68 " --> pdb=" O   VAL C 207 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 81 through 86
      removed outlier: 6.983A  pdb=" N   CYS C 185 " --> pdb=" O   LEU C  82 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   ASP C  84 " --> pdb=" O   LEU C 183 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   LEU C 183 " --> pdb=" O   ASP C  84 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   TYR C 188 " --> pdb=" O   LYS C 124 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   LYS C 124 " --> pdb=" O   TYR C 188 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ALA C 122 " --> pdb=" O   PRO C 190 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 173 through 174
    Processing sheet with id=AB8, first strand: chain 'C' and resid 253 through 255
      removed outlier: 4.204A  pdb=" N   LYS C 253 " --> pdb=" O   MET C 430 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 290 through 297
      removed outlier: 4.453A  pdb=" N   LYS C 302 " --> pdb=" O   PHE C 369 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   GLU C 368 " --> pdb=" O   LYS C 355 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   LYS C 355 " --> pdb=" O   GLU C 368 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   TRP C 385 " --> pdb=" O   HIS C 334 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   SER C 336 " --> pdb=" O   LEU C 383 " (cutoff:3.500A)
      removed outlier: 5.876A  pdb=" N   LEU C 383 " --> pdb=" O   SER C 336 " (cutoff:3.500A)
      removed outlier: 7.380A  pdb=" N   PHE C 338 " --> pdb=" O   GLY C 381 " (cutoff:3.500A)
      removed outlier: 5.832A  pdb=" N   GLY C 381 " --> pdb=" O   PHE C 338 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 425 through 426
      removed outlier: 6.484A  pdb=" N   TYR C 471 " --> pdb=" O   LEU C 480 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   GLU C 482 " --> pdb=" O   LEU C 469 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   LEU C 469 " --> pdb=" O   GLU C 482 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   LYS C 484 " --> pdb=" O   ALA C 467 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   ALA C 467 " --> pdb=" O   LYS C 484 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   ALA C 466 " --> pdb=" O   TRP C 515 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   TRP C 515 " --> pdb=" O   ALA C 466 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   LEU C 468 " --> pdb=" O   SER C 513 " (cutoff:3.500A)

    248 hydrogen bonds defined for protein.
    624 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: 3.09

  Time building geometry restraints manager: 3.08 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3676
        1.34 -     1.45: 1753
        1.45 -     1.57: 6077
        1.57 -     1.69: 0
        1.69 -     1.80: 90
  Bond restraints: 11596
  Sorted by residual:
  bond pdb=" N   ARG C 178 "
       pdb=" CA  ARG C 178 "
    ideal  model  delta    sigma   weight residual
    1.456  1.427  0.029 1.48e-02 4.57e+03 3.75e+00
  bond pdb=" CB  VAL C 106 "
       pdb=" CG1 VAL C 106 "
    ideal  model  delta    sigma   weight residual
    1.521  1.472  0.049 3.30e-02 9.18e+02 2.21e+00
  bond pdb=" C   ILE C 400 "
       pdb=" N   PRO C 401 "
    ideal  model  delta    sigma   weight residual
    1.330  1.345 -0.015 1.25e-02 6.40e+03 1.36e+00
  bond pdb=" C   ALA C  65 "
       pdb=" N   PRO C  66 "
    ideal  model  delta    sigma   weight residual
    1.334  1.361 -0.027 2.34e-02 1.83e+03 1.33e+00
  bond pdb=" C   SER B  73 "
       pdb=" N   PRO B  74 "
    ideal  model  delta    sigma   weight residual
    1.334  1.343 -0.010 8.40e-03 1.42e+04 1.33e+00
  ... (remaining 11591 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 15280
        1.76 -     3.53: 525
        3.53 -     5.29: 62
        5.29 -     7.06: 11
        7.06 -     8.82: 3
  Bond angle restraints: 15881
  Sorted by residual:
  angle pdb=" C   VAL B 221 "
        pdb=" CA  VAL B 221 "
        pdb=" CB  VAL B 221 "
      ideal   model   delta    sigma   weight residual
     109.33  115.00   -5.67 9.80e-01 1.04e+00 3.34e+01
  angle pdb=" N   VAL B 340 "
        pdb=" CA  VAL B 340 "
        pdb=" C   VAL B 340 "
      ideal   model   delta    sigma   weight residual
     113.07  106.72    6.35 1.37e+00 5.33e-01 2.15e+01
  angle pdb=" N   VAL B 221 "
        pdb=" CA  VAL B 221 "
        pdb=" C   VAL B 221 "
      ideal   model   delta    sigma   weight residual
     109.19  105.90    3.29 8.20e-01 1.49e+00 1.61e+01
  angle pdb=" CA  VAL B 221 "
        pdb=" C   VAL B 221 "
        pdb=" N   PRO B 222 "
      ideal   model   delta    sigma   weight residual
     116.57  119.95   -3.38 9.80e-01 1.04e+00 1.19e+01
  angle pdb=" N   ARG C 178 "
        pdb=" CA  ARG C 178 "
        pdb=" C   ARG C 178 "
      ideal   model   delta    sigma   weight residual
     107.95  100.88    7.07 2.14e+00 2.18e-01 1.09e+01
  ... (remaining 15876 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 6324
       17.44 -    34.89: 463
       34.89 -    52.33: 89
       52.33 -    69.77: 12
       69.77 -    87.22: 7
  Dihedral angle restraints: 6895
    sinusoidal: 2693
      harmonic: 4202
  Sorted by residual:
  dihedral pdb=" CA  PHE C 217 "
           pdb=" C   PHE C 217 "
           pdb=" N   LEU C 218 "
           pdb=" CA  LEU C 218 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.74  -24.26     0      5.00e+00 4.00e-02 2.35e+01
  dihedral pdb=" CA  VAL C 340 "
           pdb=" C   VAL C 340 "
           pdb=" N   ASP C 341 "
           pdb=" CA  ASP C 341 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.37  -23.63     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" CA  ARG A 182 "
           pdb=" C   ARG A 182 "
           pdb=" N   LEU A 183 "
           pdb=" CA  LEU A 183 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.90   20.10     0      5.00e+00 4.00e-02 1.62e+01
  ... (remaining 6892 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 954
       0.035 -    0.070: 504
       0.070 -    0.104: 180
       0.104 -    0.139: 122
       0.139 -    0.174: 23
  Chirality restraints: 1783
  Sorted by residual:
  chirality pdb=" CB  THR A 497 "
            pdb=" CA  THR A 497 "
            pdb=" OG1 THR A 497 "
            pdb=" CG2 THR A 497 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.57e-01
  chirality pdb=" CA  VAL C 256 "
            pdb=" N   VAL C 256 "
            pdb=" C   VAL C 256 "
            pdb=" CB  VAL C 256 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.17 2.00e-01 2.50e+01 7.56e-01
  chirality pdb=" CB  ILE B 126 "
            pdb=" CA  ILE B 126 "
            pdb=" CG1 ILE B 126 "
            pdb=" CG2 ILE B 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.52e-01
  ... (remaining 1780 not shown)

  Planarity restraints: 2112
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 212 "    0.055 5.00e-02 4.00e+02   8.39e-02 1.13e+01
        pdb=" N   PRO A 213 "   -0.145 5.00e-02 4.00e+02
        pdb=" CA  PRO A 213 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 213 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 212 "   -0.053 5.00e-02 4.00e+02   8.05e-02 1.04e+01
        pdb=" N   PRO B 213 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO B 213 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO B 213 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 212 "    0.049 5.00e-02 4.00e+02   7.37e-02 8.69e+00
        pdb=" N   PRO C 213 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO C 213 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO C 213 "    0.041 5.00e-02 4.00e+02
  ... (remaining 2109 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 106
        2.63 -     3.20: 8951
        3.20 -     3.77: 15624
        3.77 -     4.33: 22055
        4.33 -     4.90: 37821
  Nonbonded interactions: 84557
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG C 394 "
            pdb=" OD1 ASN C 439 "
     model   vdw
     2.067 3.120
  nonbonded pdb=" NZ  LYS A 294 "
            pdb=" OD2 ASP A 378 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" CE  LYS A 294 "
            pdb=" OD2 ASP A 378 "
     model   vdw
     2.300 3.440
  nonbonded pdb=" O   ASN C 108 "
            pdb=" OG  SER C 212 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OG  SER C 319 "
            pdb=" O   ALA C 321 "
     model   vdw
     2.330 3.040
  ... (remaining 84552 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 33 through 404 or resid 412 through 526))
  selection = (chain 'B' and (resid 33 through 404 or resid 412 through 526))
  selection = (chain 'C' and (resid 33 through 193 or resid 200 through 404 or resid 412 throu \ 
gh 526))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.500
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     27.050
  Find NCS groups from input model:        0.520
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
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      :  0.006   0.055  11596  Z= 0.248
  Angle     :  0.753   8.822  15881  Z= 0.430
  Chirality :  0.054   0.174   1783
  Planarity :  0.009   0.084   2112
  Dihedral  : 12.958  87.217   4185
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  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: -3.26 (0.18), residues: 1457
  helix: -4.17 (0.26), residues: 71
  sheet: -1.49 (0.24), residues: 387
  loop : -2.44 (0.16), residues: 999

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 385 
 HIS   0.003   0.001   HIS C 470 
 PHE   0.027   0.002   PHE C  83 
 TYR   0.009   0.002   TYR A 102 
 ARG   0.006   0.000   ARG C 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25834 (  246)
  hydrogen bonds       : angle       9.72152 (  624)
  covalent geometry    : bond        0.00582 (11596)
  covalent geometry    : angle       0.75276 (15881)

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

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

  2914 Ramachandran restraints generated.
    1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2914 Ramachandran restraints generated.
    1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 305
  time to evaluate  : 1.195 
Fit side-chains
REVERT: B   57 TRP cc_start: 0.8875 (m100) cc_final: 0.8604 (m100)
REVERT: B  192 ARG cc_start: 0.7941 (mmt-90) cc_final: 0.7414 (mtt180)
REVERT: B  308 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8405 (mm-30)
REVERT: B  430 MET cc_start: 0.8966 (mmm) cc_final: 0.8563 (mmm)
REVERT: A  252 ASN cc_start: 0.8622 (t0) cc_final: 0.8374 (t0)
REVERT: A  396 ASP cc_start: 0.8761 (t0) cc_final: 0.8511 (t0)
REVERT: A  458 GLN cc_start: 0.8465 (tt0) cc_final: 0.8223 (tt0)
REVERT: A  478 ARG cc_start: 0.8080 (mtp180) cc_final: 0.7860 (mmm160)
REVERT: C  290 ARG cc_start: 0.8624 (mmm-85) cc_final: 0.8330 (mmm-85)
REVERT: C  338 PHE cc_start: 0.8077 (p90) cc_final: 0.7767 (p90)
REVERT: C  349 MET cc_start: 0.8446 (mmm) cc_final: 0.8209 (mmm)
REVERT: C  457 GLU cc_start: 0.7006 (tp30) cc_final: 0.6790 (tp30)
REVERT: C  465 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7651 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 305
  average time/residue: 0.2249
  time to fit residues: 97.1251
Evaluate side-chains
  261 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 1.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 123 optimal weight:    4.9990
   chunk 110 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 37 optimal weight:   10.0000
   chunk 74 optimal weight:    8.9990
   chunk 59 optimal weight:    7.9990
   chunk 114 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 69 optimal weight:    0.4980
   chunk 85 optimal weight:    8.9990
   chunk 132 optimal weight:    9.9990
   overall best weight:    4.4988

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

Flipped N/Q/H residues before XYZ refinement:
B 261 ASN
B 315 HIS
B 343 ASN
A  60 ASN
A 108 ASN
A 357 ASN
A 458 GLN
C  75 ASN
C  76 ASN
C  86 HIS
C 173 HIS
C 479 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.111311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.086637 restraints weight = 16234.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.2837 rms_B_bonded: 2.62
r_work: 0.2724 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2582 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.1115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11596  Z= 0.168
  Angle     :  0.570   8.062  15881  Z= 0.288
  Chirality :  0.047   0.160   1783
  Planarity :  0.006   0.058   2112
  Dihedral  :  4.856  22.602   1546
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  7.98 %
    Favored  : 90.82 %
  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: -2.55 (0.19), residues: 1457
  helix: -3.27 (0.38), residues: 79
  sheet: -1.17 (0.24), residues: 398
  loop : -1.87 (0.17), residues: 980

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 385 
 HIS   0.006   0.001   HIS C  86 
 PHE   0.019   0.001   PHE C  83 
 TYR   0.009   0.001   TYR C 520 
 ARG   0.003   0.000   ARG C 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04179 (  246)
  hydrogen bonds       : angle       6.42617 (  624)
  covalent geometry    : bond        0.00407 (11596)
  covalent geometry    : angle       0.57049 (15881)

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

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

  2914 Ramachandran restraints generated.
    1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2914 Ramachandran restraints generated.
    1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 287
  time to evaluate  : 1.258 
Fit side-chains
REVERT: B   57 TRP cc_start: 0.9128 (m100) cc_final: 0.8880 (m100)
REVERT: B  192 ARG cc_start: 0.8418 (mmt-90) cc_final: 0.7581 (mtt180)
REVERT: B  231 GLN cc_start: 0.8379 (tt0) cc_final: 0.8021 (tp40)
REVERT: B  237 ILE cc_start: 0.9441 (mt) cc_final: 0.9113 (mm)
REVERT: B  294 LYS cc_start: 0.8482 (mtmm) cc_final: 0.8038 (mttp)
REVERT: A  252 ASN cc_start: 0.8900 (t0) cc_final: 0.8640 (t0)
REVERT: A  396 ASP cc_start: 0.8930 (t0) cc_final: 0.8632 (t0)
REVERT: A  458 GLN cc_start: 0.8785 (tt0) cc_final: 0.8565 (tt0)
REVERT: C  236 ASN cc_start: 0.8835 (t0) cc_final: 0.8561 (t0)
REVERT: C  465 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8471 (mt-10)
REVERT: C  479 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.7883 (t0)
  outliers start: 15
  outliers final: 11
  residues processed: 294
  average time/residue: 0.2236
  time to fit residues: 94.6760
Evaluate side-chains
  279 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 267
  time to evaluate  : 1.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  315 HIS
Chi-restraints excluded: chain B residue  317 PHE
Chi-restraints excluded: chain B residue  319 SER
Chi-restraints excluded: chain A residue   96 GLN
Chi-restraints excluded: chain A residue  108 ASN
Chi-restraints excluded: chain A residue  158 GLU
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain C residue  237 ILE
Chi-restraints excluded: chain C residue  328 ILE
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  479 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 107 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9990
   chunk 4 optimal weight:   10.0000
   chunk 5 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 81 optimal weight:   20.0000
   chunk 99 optimal weight:    7.9990
   chunk 129 optimal weight:   20.0000
   chunk 75 optimal weight:   20.0000
   chunk 101 optimal weight:   10.0000
   chunk 118 optimal weight:    8.9990
   overall best weight:    3.9586

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

Flipped N/Q/H residues before XYZ refinement:
** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  60 ASN
A 108 ASN
C  86 HIS
C 479 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.111496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.086586 restraints weight = 16444.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 2.65
r_work: 0.2721 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2581 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.1362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11596  Z= 0.148
  Angle     :  0.538   7.620  15881  Z= 0.268
  Chirality :  0.046   0.157   1783
  Planarity :  0.005   0.053   2112
  Dihedral  :  4.601  21.554   1546
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 10.85 %
    Favored  : 87.79 %
  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: -2.13 (0.20), residues: 1457
  helix: -2.82 (0.43), residues: 79
  sheet: -0.90 (0.24), residues: 396
  loop : -1.58 (0.18), residues: 982

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 385 
 HIS   0.012   0.001   HIS B 315 
 PHE   0.017   0.001   PHE C  83 
 TYR   0.010   0.001   TYR C 520 
 ARG   0.006   0.000   ARG B 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03603 (  246)
  hydrogen bonds       : angle       5.94902 (  624)
  covalent geometry    : bond        0.00362 (11596)
  covalent geometry    : angle       0.53771 (15881)

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

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

  2914 Ramachandran restraints generated.
    1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2914 Ramachandran restraints generated.
    1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 271
  time to evaluate  : 2.178 
Fit side-chains
REVERT: B   28 ASN cc_start: 0.8900 (t0) cc_final: 0.8589 (t0)
REVERT: B   57 TRP cc_start: 0.9104 (m100) cc_final: 0.8832 (m100)
REVERT: B  192 ARG cc_start: 0.8406 (mmt-90) cc_final: 0.7574 (mtt180)
REVERT: B  231 GLN cc_start: 0.8321 (tt0) cc_final: 0.8000 (tt0)
REVERT: B  237 ILE cc_start: 0.9454 (mt) cc_final: 0.9114 (mm)
REVERT: A  396 ASP cc_start: 0.8917 (t0) cc_final: 0.8609 (t0)
REVERT: C  236 ASN cc_start: 0.8844 (t0) cc_final: 0.8589 (t0)
REVERT: C  302 LYS cc_start: 0.8169 (ttmm) cc_final: 0.7761 (tppt)
  outliers start: 17
  outliers final: 13
  residues processed: 277
  average time/residue: 0.2612
  time to fit residues: 104.8967
Evaluate side-chains
  271 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 258
  time to evaluate  : 1.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  315 HIS
Chi-restraints excluded: chain B residue  317 PHE
Chi-restraints excluded: chain B residue  319 SER
Chi-restraints excluded: chain A residue   96 GLN
Chi-restraints excluded: chain A residue  108 ASN
Chi-restraints excluded: chain A residue  158 GLU
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain C residue  254 MET
Chi-restraints excluded: chain C residue  328 ILE
Chi-restraints excluded: chain C residue  376 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 93 optimal weight:   20.0000
   chunk 110 optimal weight:    7.9990
   chunk 124 optimal weight:   40.0000
   chunk 37 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9980
   chunk 74 optimal weight:    6.9990
   chunk 68 optimal weight:    0.0970
   chunk 51 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 5 optimal weight:    0.5980
   chunk 118 optimal weight:    0.9990
   overall best weight:    1.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 175 ASN
** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  60 ASN
A 108 ASN
A 236 ASN
C  90 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.109770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.084688 restraints weight = 16367.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.2921 rms_B_bonded: 2.70
r_work: 0.2809 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2667 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  11596  Z= 0.094
  Angle     :  0.498   7.503  15881  Z= 0.246
  Chirality :  0.045   0.155   1783
  Planarity :  0.005   0.048   2112
  Dihedral  :  4.291  20.470   1546
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 12.53 %
    Favored  : 86.11 %
  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: -1.72 (0.20), residues: 1457
  helix: -2.43 (0.46), residues: 79
  sheet: -0.62 (0.24), residues: 402
  loop : -1.30 (0.18), residues: 976

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 385 
 HIS   0.006   0.001   HIS C  86 
 PHE   0.014   0.001   PHE C  83 
 TYR   0.009   0.001   TYR C 520 
 ARG   0.002   0.000   ARG A 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02931 (  246)
  hydrogen bonds       : angle       5.57152 (  624)
  covalent geometry    : bond        0.00234 (11596)
  covalent geometry    : angle       0.49768 (15881)

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

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

  2914 Ramachandran restraints generated.
    1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2914 Ramachandran restraints generated.
    1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 283
  time to evaluate  : 1.203 
Fit side-chains
REVERT: B   57 TRP cc_start: 0.9055 (m100) cc_final: 0.8804 (m100)
REVERT: B  192 ARG cc_start: 0.8327 (mmt-90) cc_final: 0.7416 (mtt180)
REVERT: B  231 GLN cc_start: 0.8368 (tt0) cc_final: 0.8058 (tt0)
REVERT: B  237 ILE cc_start: 0.9441 (mt) cc_final: 0.9102 (mm)
REVERT: A  236 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.8840 (t0)
REVERT: A  396 ASP cc_start: 0.8912 (t0) cc_final: 0.8630 (t0)
REVERT: A  458 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8471 (tt0)
REVERT: C  236 ASN cc_start: 0.8868 (t0) cc_final: 0.8668 (t0)
REVERT: C  287 GLN cc_start: 0.9009 (mt0) cc_final: 0.8732 (mt0)
REVERT: C  297 SER cc_start: 0.7965 (m) cc_final: 0.7318 (t)
REVERT: C  302 LYS cc_start: 0.8028 (ttmm) cc_final: 0.7536 (tppt)
  outliers start: 17
  outliers final: 10
  residues processed: 288
  average time/residue: 0.2204
  time to fit residues: 91.5536
Evaluate side-chains
  285 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 273
  time to evaluate  : 1.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  315 HIS
Chi-restraints excluded: chain B residue  317 PHE
Chi-restraints excluded: chain A residue   96 GLN
Chi-restraints excluded: chain A residue  158 GLU
Chi-restraints excluded: chain A residue  236 ASN
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  458 GLN
Chi-restraints excluded: chain C residue  158 GLU
Chi-restraints excluded: chain C residue  237 ILE
Chi-restraints excluded: chain C residue  254 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 133 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9980
   chunk 118 optimal weight:    7.9990
   chunk 144 optimal weight:    8.9990
   chunk 34 optimal weight:    7.9990
   chunk 106 optimal weight:    9.9990
   chunk 108 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   chunk 98 optimal weight:    0.0770
   overall best weight:    3.4144

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

Flipped N/Q/H residues before XYZ refinement:
B 315 HIS
** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  60 ASN
A 118 ASN
A 236 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.110053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.085177 restraints weight = 16354.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.2898 rms_B_bonded: 2.64
r_work: 0.2788 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2649 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11596  Z= 0.128
  Angle     :  0.510   7.855  15881  Z= 0.251
  Chirality :  0.046   0.159   1783
  Planarity :  0.005   0.046   2112
  Dihedral  :  4.220  19.929   1546
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 12.93 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.21), residues: 1457
  helix: -2.23 (0.47), residues: 79
  sheet: -0.51 (0.25), residues: 400
  loop : -1.10 (0.19), residues: 978

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 385 
 HIS   0.006   0.001   HIS C  86 
 PHE   0.014   0.001   PHE C  83 
 TYR   0.005   0.001   TYR A 471 
 ARG   0.002   0.000   ARG A 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02950 (  246)
  hydrogen bonds       : angle       5.39478 (  624)
  covalent geometry    : bond        0.00319 (11596)
  covalent geometry    : angle       0.51037 (15881)

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

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

  2914 Ramachandran restraints generated.
    1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2914 Ramachandran restraints generated.
    1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 268
  time to evaluate  : 1.213 
Fit side-chains
REVERT: B   57 TRP cc_start: 0.9073 (m100) cc_final: 0.8833 (m100)
REVERT: B  192 ARG cc_start: 0.8347 (mmt-90) cc_final: 0.7473 (mtt180)
REVERT: B  231 GLN cc_start: 0.8338 (tt0) cc_final: 0.8038 (tt0)
REVERT: B  237 ILE cc_start: 0.9455 (mt) cc_final: 0.9116 (mm)
REVERT: B  422 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7839 (t80)
REVERT: A  396 ASP cc_start: 0.8903 (t0) cc_final: 0.8694 (t0)
REVERT: A  518 ARG cc_start: 0.8572 (ptp-110) cc_final: 0.7831 (ptm-80)
REVERT: C  287 GLN cc_start: 0.9037 (mt0) cc_final: 0.8750 (mt0)
REVERT: C  302 LYS cc_start: 0.8045 (ttmm) cc_final: 0.7808 (tppt)
  outliers start: 23
  outliers final: 16
  residues processed: 276
  average time/residue: 0.2225
  time to fit residues: 88.1301
Evaluate side-chains
  277 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 260
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  315 HIS
Chi-restraints excluded: chain B residue  317 PHE
Chi-restraints excluded: chain B residue  422 PHE
Chi-restraints excluded: chain A residue   96 GLN
Chi-restraints excluded: chain A residue  158 GLU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  236 ASN
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  457 GLU
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain C residue  158 GLU
Chi-restraints excluded: chain C residue  254 MET
Chi-restraints excluded: chain C residue  328 ILE
Chi-restraints excluded: chain C residue  355 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 33 optimal weight:   20.0000
   chunk 139 optimal weight:    6.9990
   chunk 69 optimal weight:    3.9990
   chunk 39 optimal weight:    8.9990
   chunk 48 optimal weight:    4.9990
   chunk 108 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 42 optimal weight:   10.0000
   chunk 72 optimal weight:    5.9990
   chunk 89 optimal weight:    9.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  60 ASN
A 236 ASN
C 503 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.110976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.086077 restraints weight = 16578.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.2891 rms_B_bonded: 2.65
r_work: 0.2781 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2641 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.1682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  11596  Z= 0.192
  Angle     :  0.544   8.245  15881  Z= 0.268
  Chirality :  0.047   0.154   1783
  Planarity :  0.005   0.044   2112
  Dihedral  :  4.346  19.926   1546
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.57 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.37 (0.21), residues: 1457
  helix: -2.16 (0.47), residues: 79
  sheet: -0.45 (0.25), residues: 391
  loop : -1.01 (0.19), residues: 987

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 385 
 HIS   0.007   0.001   HIS B 315 
 PHE   0.018   0.001   PHE C 369 
 TYR   0.010   0.001   TYR C 520 
 ARG   0.007   0.000   ARG C 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03232 (  246)
  hydrogen bonds       : angle       5.40109 (  624)
  covalent geometry    : bond        0.00473 (11596)
  covalent geometry    : angle       0.54443 (15881)

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

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

  2914 Ramachandran restraints generated.
    1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2914 Ramachandran restraints generated.
    1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 257
  time to evaluate  : 1.383 
Fit side-chains
REVERT: B   57 TRP cc_start: 0.9070 (m100) cc_final: 0.8804 (m100)
REVERT: B  192 ARG cc_start: 0.8381 (mmt-90) cc_final: 0.7566 (mtt180)
REVERT: B  231 GLN cc_start: 0.8377 (tt0) cc_final: 0.8081 (tt0)
REVERT: B  422 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7826 (t80)
REVERT: A  396 ASP cc_start: 0.8894 (t0) cc_final: 0.8690 (t0)
REVERT: C  302 LYS cc_start: 0.8094 (ttmm) cc_final: 0.7735 (tppt)
  outliers start: 25
  outliers final: 19
  residues processed: 267
  average time/residue: 0.2313
  time to fit residues: 88.4397
Evaluate side-chains
  276 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 256
  time to evaluate  : 1.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue   99 SER
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  315 HIS
Chi-restraints excluded: chain B residue  317 PHE
Chi-restraints excluded: chain B residue  422 PHE
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain A residue   96 GLN
Chi-restraints excluded: chain A residue  158 GLU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  236 ASN
Chi-restraints excluded: chain A residue  457 GLU
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain C residue  158 GLU
Chi-restraints excluded: chain C residue  210 CYS
Chi-restraints excluded: chain C residue  328 ILE
Chi-restraints excluded: chain C residue  355 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 85 optimal weight:    0.6980
   chunk 35 optimal weight:   10.0000
   chunk 33 optimal weight:    5.9990
   chunk 94 optimal weight:    3.9990
   chunk 114 optimal weight:    5.9990
   chunk 126 optimal weight:    0.0770
   chunk 65 optimal weight:    5.9990
   chunk 143 optimal weight:    0.0060
   chunk 73 optimal weight:   10.0000
   chunk 15 optimal weight:    0.0070
   chunk 125 optimal weight:    9.9990
   overall best weight:    0.9574

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

Flipped N/Q/H residues before XYZ refinement:
** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.114216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.089944 restraints weight = 16215.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 2.55
r_work: 0.2770 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2632 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  11596  Z= 0.078
  Angle     :  0.500   9.459  15881  Z= 0.243
  Chirality :  0.045   0.157   1783
  Planarity :  0.005   0.044   2112
  Dihedral  :  4.033  18.977   1546
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 14.37 %
    Favored  : 84.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.21), residues: 1457
  helix: -1.70 (0.50), residues: 79
  sheet: -0.27 (0.25), residues: 401
  loop : -0.83 (0.19), residues: 977

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 385 
 HIS   0.005   0.000   HIS C  86 
 PHE   0.018   0.001   PHE C 369 
 TYR   0.009   0.001   TYR C 520 
 ARG   0.006   0.000   ARG C 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02501 (  246)
  hydrogen bonds       : angle       5.08755 (  624)
  covalent geometry    : bond        0.00193 (11596)
  covalent geometry    : angle       0.50000 (15881)

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

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

  2914 Ramachandran restraints generated.
    1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2914 Ramachandran restraints generated.
    1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 275
  time to evaluate  : 1.200 
Fit side-chains
REVERT: B   57 TRP cc_start: 0.9047 (m100) cc_final: 0.8834 (m100)
REVERT: B  192 ARG cc_start: 0.8329 (mmt-90) cc_final: 0.7585 (mtt180)
REVERT: B  231 GLN cc_start: 0.8282 (tt0) cc_final: 0.7972 (tt0)
REVERT: B  374 ASP cc_start: 0.8324 (t70) cc_final: 0.7529 (p0)
REVERT: A  146 MET cc_start: 0.9269 (mtt) cc_final: 0.9047 (mtt)
REVERT: A  518 ARG cc_start: 0.8618 (ptp-110) cc_final: 0.7848 (ptm-80)
REVERT: C  287 GLN cc_start: 0.9119 (mt0) cc_final: 0.8844 (mt0)
REVERT: C  302 LYS cc_start: 0.8111 (ttmm) cc_final: 0.7770 (tppt)
  outliers start: 16
  outliers final: 12
  residues processed: 283
  average time/residue: 0.2620
  time to fit residues: 105.9779
Evaluate side-chains
  275 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 263
  time to evaluate  : 1.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  315 HIS
Chi-restraints excluded: chain B residue  317 PHE
Chi-restraints excluded: chain A residue   96 GLN
Chi-restraints excluded: chain A residue  158 GLU
Chi-restraints excluded: chain A residue  236 ASN
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  458 GLN
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain C residue  237 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 123 optimal weight:    5.9990
   chunk 39 optimal weight:    0.5980
   chunk 99 optimal weight:    0.9990
   chunk 26 optimal weight:    8.9990
   chunk 22 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 46 optimal weight:   10.0000
   chunk 114 optimal weight:    7.9990
   chunk 40 optimal weight:    4.9990
   chunk 100 optimal weight:    8.9990
   chunk 29 optimal weight:    0.0670
   overall best weight:    2.5324

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

Flipped N/Q/H residues before XYZ refinement:
** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 458 GLN
A 236 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.112465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.088162 restraints weight = 16326.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.2869 rms_B_bonded: 2.58
r_work: 0.2759 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2622 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11596  Z= 0.106
  Angle     :  0.509   8.701  15881  Z= 0.245
  Chirality :  0.045   0.150   1783
  Planarity :  0.005   0.043   2112
  Dihedral  :  3.996  18.667   1546
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.45 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.92 (0.21), residues: 1457
  helix: -1.47 (0.51), residues: 79
  sheet: -0.07 (0.26), residues: 382
  loop : -0.76 (0.19), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 385 
 HIS   0.006   0.001   HIS A 412 
 PHE   0.013   0.001   PHE C  83 
 TYR   0.005   0.001   TYR C 471 
 ARG   0.005   0.000   ARG C 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02612 (  246)
  hydrogen bonds       : angle       5.03854 (  624)
  covalent geometry    : bond        0.00265 (11596)
  covalent geometry    : angle       0.50881 (15881)

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

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

  2914 Ramachandran restraints generated.
    1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2914 Ramachandran restraints generated.
    1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 265
  time to evaluate  : 1.259 
Fit side-chains
REVERT: B   57 TRP cc_start: 0.9058 (m100) cc_final: 0.8826 (m100)
REVERT: B  192 ARG cc_start: 0.8336 (mmt-90) cc_final: 0.7535 (mtt180)
REVERT: B  231 GLN cc_start: 0.8316 (tt0) cc_final: 0.8052 (tt0)
REVERT: B  341 ASP cc_start: 0.8513 (t0) cc_final: 0.8179 (t70)
REVERT: B  374 ASP cc_start: 0.8331 (t70) cc_final: 0.7505 (p0)
REVERT: B  422 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.7869 (t80)
REVERT: A  146 MET cc_start: 0.9263 (mtt) cc_final: 0.9056 (mtt)
REVERT: A  518 ARG cc_start: 0.8629 (ptp-110) cc_final: 0.8046 (ptm-80)
REVERT: C  246 ARG cc_start: 0.8859 (mtm180) cc_final: 0.8174 (mtp180)
REVERT: C  287 GLN cc_start: 0.9132 (mt0) cc_final: 0.8858 (mt0)
REVERT: C  302 LYS cc_start: 0.8069 (ttmm) cc_final: 0.7775 (tppt)
  outliers start: 19
  outliers final: 15
  residues processed: 276
  average time/residue: 0.2228
  time to fit residues: 87.5917
Evaluate side-chains
  276 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 260
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  186 MET
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  315 HIS
Chi-restraints excluded: chain B residue  317 PHE
Chi-restraints excluded: chain B residue  422 PHE
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain A residue   96 GLN
Chi-restraints excluded: chain A residue  158 GLU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  457 GLU
Chi-restraints excluded: chain A residue  458 GLN
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain C residue  158 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 134 optimal weight:   20.0000
   chunk 92 optimal weight:    7.9990
   chunk 129 optimal weight:    7.9990
   chunk 2 optimal weight:    0.3980
   chunk 42 optimal weight:    0.0070
   chunk 32 optimal weight:    7.9990
   chunk 10 optimal weight:   20.0000
   chunk 127 optimal weight:   20.0000
   chunk 82 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0980
   overall best weight:    2.3002

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

Flipped N/Q/H residues before XYZ refinement:
** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 442 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.113655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.089431 restraints weight = 16132.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.2825 rms_B_bonded: 2.57
r_work: 0.2715 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2579 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.2012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11596  Z= 0.099
  Angle     :  0.506   9.009  15881  Z= 0.243
  Chirality :  0.045   0.151   1783
  Planarity :  0.005   0.043   2112
  Dihedral  :  3.916  18.549   1546
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 14.60 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.21), residues: 1457
  helix: -1.12 (0.53), residues: 79
  sheet: -0.15 (0.25), residues: 399
  loop : -0.61 (0.20), residues: 979

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 385 
 HIS   0.006   0.001   HIS A 412 
 PHE   0.020   0.001   PHE C 369 
 TYR   0.006   0.001   TYR C 471 
 ARG   0.005   0.000   ARG C 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02571 (  246)
  hydrogen bonds       : angle       4.95056 (  624)
  covalent geometry    : bond        0.00249 (11596)
  covalent geometry    : angle       0.50599 (15881)

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

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

  2914 Ramachandran restraints generated.
    1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2914 Ramachandran restraints generated.
    1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 270
  time to evaluate  : 1.222 
Fit side-chains
REVERT: B   57 TRP cc_start: 0.9056 (m100) cc_final: 0.8824 (m100)
REVERT: B  192 ARG cc_start: 0.8331 (mmt-90) cc_final: 0.7532 (mtt180)
REVERT: B  231 GLN cc_start: 0.8257 (tt0) cc_final: 0.7967 (tt0)
REVERT: B  341 ASP cc_start: 0.8588 (t0) cc_final: 0.8216 (t70)
REVERT: B  374 ASP cc_start: 0.8257 (t70) cc_final: 0.7472 (p0)
REVERT: B  422 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7878 (t80)
REVERT: A  518 ARG cc_start: 0.8608 (ptp-110) cc_final: 0.8007 (ptm-80)
REVERT: C  287 GLN cc_start: 0.9145 (mt0) cc_final: 0.8862 (mt0)
REVERT: C  302 LYS cc_start: 0.8037 (ttmm) cc_final: 0.7758 (tppt)
  outliers start: 18
  outliers final: 14
  residues processed: 279
  average time/residue: 0.2458
  time to fit residues: 97.2295
Evaluate side-chains
  276 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 261
  time to evaluate  : 1.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  186 MET
Chi-restraints excluded: chain B residue  315 HIS
Chi-restraints excluded: chain B residue  317 PHE
Chi-restraints excluded: chain B residue  422 PHE
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain A residue   96 GLN
Chi-restraints excluded: chain A residue  158 GLU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  458 GLN
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain C residue  158 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 106 optimal weight:    9.9990
   chunk 112 optimal weight:    8.9990
   chunk 43 optimal weight:    9.9990
   chunk 57 optimal weight:   10.0000
   chunk 109 optimal weight:   10.0000
   chunk 28 optimal weight:    8.9990
   chunk 138 optimal weight:    0.0040
   chunk 84 optimal weight:   10.0000
   chunk 52 optimal weight:    0.7980
   chunk 3 optimal weight:    7.9990
   chunk 130 optimal weight:   10.0000
   overall best weight:    5.3598

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

Flipped N/Q/H residues before XYZ refinement:
** B 356 GLN ** 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 = 0.3214 r_free = 0.3214 target = 0.111230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.086704 restraints weight = 16471.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.2705 rms_B_bonded: 2.64
r_work: 0.2592 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2456 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  11596  Z= 0.186
  Angle     :  0.549   8.395  15881  Z= 0.268
  Chirality :  0.047   0.153   1783
  Planarity :  0.005   0.041   2112
  Dihedral  :  4.190  18.549   1546
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.29 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.85 (0.21), residues: 1457
  helix: -1.22 (0.53), residues: 79
  sheet: -0.18 (0.26), residues: 387
  loop : -0.65 (0.19), residues: 991

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  57 
 HIS   0.006   0.001   HIS A 412 
 PHE   0.015   0.001   PHE C  83 
 TYR   0.009   0.001   TYR C 520 
 ARG   0.005   0.000   ARG C 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03145 (  246)
  hydrogen bonds       : angle       5.15518 (  624)
  covalent geometry    : bond        0.00462 (11596)
  covalent geometry    : angle       0.54944 (15881)

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

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

  2914 Ramachandran restraints generated.
    1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2914 Ramachandran restraints generated.
    1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 257
  time to evaluate  : 2.198 
Fit side-chains
   revert: symmetry clash
REVERT: B  192 ARG cc_start: 0.8264 (mmt-90) cc_final: 0.7327 (mtt180)
REVERT: B  231 GLN cc_start: 0.8288 (tt0) cc_final: 0.7958 (tt0)
REVERT: B  341 ASP cc_start: 0.8507 (t0) cc_final: 0.7987 (t0)
REVERT: B  422 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.7843 (t80)
REVERT: C  302 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7683 (tppt)
  outliers start: 20
  outliers final: 16
  residues processed: 265
  average time/residue: 0.3198
  time to fit residues: 123.0300
Evaluate side-chains
  269 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 252
  time to evaluate  : 2.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  186 MET
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  315 HIS
Chi-restraints excluded: chain B residue  317 PHE
Chi-restraints excluded: chain B residue  422 PHE
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue   96 GLN
Chi-restraints excluded: chain A residue  158 GLU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  453 SER
Chi-restraints excluded: chain A residue  457 GLU
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain C residue  158 GLU
Chi-restraints excluded: chain C residue  400 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 55 optimal weight:    9.9990
   chunk 92 optimal weight:   10.0000
   chunk 30 optimal weight:    0.8980
   chunk 77 optimal weight:    0.0570
   chunk 26 optimal weight:    6.9990
   chunk 31 optimal weight:   10.0000
   chunk 51 optimal weight:   20.0000
   chunk 11 optimal weight:    4.9990
   chunk 41 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    2.7904

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

Flipped N/Q/H residues before XYZ refinement:
** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.110317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.086196 restraints weight = 16340.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 2.55
r_work: 0.2745 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2607 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11596  Z= 0.115
  Angle     :  0.514   7.331  15881  Z= 0.250
  Chirality :  0.046   0.152   1783
  Planarity :  0.005   0.041   2112
  Dihedral  :  4.043  18.238   1546
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 14.68 %
    Favored  : 83.64 %
  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: -0.69 (0.21), residues: 1457
  helix: -1.01 (0.53), residues: 79
  sheet: -0.03 (0.26), residues: 377
  loop : -0.57 (0.20), residues: 1001

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 385 
 HIS   0.006   0.001   HIS A 412 
 PHE   0.013   0.001   PHE B 369 
 TYR   0.010   0.001   TYR C 520 
 ARG   0.005   0.000   ARG C 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02697 (  246)
  hydrogen bonds       : angle       5.01236 (  624)
  covalent geometry    : bond        0.00291 (11596)
  covalent geometry    : angle       0.51403 (15881)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6132.88 seconds
wall clock time: 108 minutes 27.40 seconds (6507.40 seconds total)