Starting phenix.real_space_refine
on Tue Mar  3 22:37:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rxd_24729/03_2026/7rxd_24729.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rxd_24729/03_2026/7rxd_24729.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rxd_24729/03_2026/7rxd_24729.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rxd_24729/03_2026/7rxd_24729.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rxd_24729/03_2026/7rxd_24729.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rxd_24729/03_2026/7rxd_24729.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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      31      5.16       5
     C    5749      2.51       5
     N    1490      2.21       5
     O    1737      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9007
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 3433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 439, 3433
          Classifications: {'peptide': 439}
          Link IDs: {'PTRANS': 24, 'TRANS': 414}
          Chain breaks: 4
    Chain: "H"
      Number of atoms: 1582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1582
          Classifications: {'peptide': 207}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 192}
          Chain breaks: 2
    Chain: "L"
      Number of atoms: 1588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1588
          Classifications: {'peptide': 204}
          Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 194}
          Chain breaks: 2
    Chain: "N"
      Number of atoms: 990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 990
          Classifications: {'peptide': 125}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "R"
      Number of atoms: 1391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 173, 1391
          Classifications: {'peptide': 173}
          Link IDs: {'PTRANS': 9, 'TRANS': 163}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'GLC': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.33, per 1000 atoms: 0.26
  Number of scatterers: 9007
  At special positions: 0
  Unit cell: (118.72, 133.56, 111.3, 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      31     16.00
     O    1737      8.00
     N    1490      7.00
     C    5749      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 150 " - pdb=" SG  CYS H 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 139 " - pdb=" SG  CYS L 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 379 " - pdb=" SG  CYS R 432 " distance=2.05
    Simple disulfide: pdb=" SG  CYS R 480 " - pdb=" SG  CYS R 488 " 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
  Links applied
    ALPHA1-4
      " GLC A   1 " - " GLC A   2 "
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 329.8 milliseconds
  

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2126

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 22 sheets defined
      27.9% alpha, 33.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'B' and resid 17 through 28
    Processing helix  chain 'B' and resid 43 through 52
      Proline residue:  B  49  - end of helix
    Processing helix  chain 'B' and resid 64 through 74
      removed outlier: 4.055A  pdb=" N   PHE B  68 " --> pdb=" O   ALA B  64 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLY B  69 " --> pdb=" O   HIS B  65 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   GLY B  70 " --> pdb=" O   ASP B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 89
    Processing helix  chain 'B' and resid 91 through 98
      removed outlier: 3.553A  pdb=" N   TRP B  95 " --> pdb=" O   TYR B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 141
      removed outlier: 4.490A  pdb=" N   ALA B 135 " --> pdb=" O   GLU B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 164
      removed outlier: 3.923A  pdb=" N   THR B 158 " --> pdb=" O   GLU B 154 " (cutoff:3.500A)
      Proline residue:  B 160  - end of helix
    Processing helix  chain 'B' and resid 182 through 185
      removed outlier: 4.399A  pdb=" N   ASP B 185 " --> pdb=" O   VAL B 182 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 182 through 185'
    Processing helix  chain 'B' and resid 186 through 202
    Processing helix  chain 'B' and resid 210 through 220
    Processing helix  chain 'B' and resid 229 through 231
      No H-bonds generated for 'chain 'B' and resid 229 through 231'
    Processing helix  chain 'B' and resid 232 through 240
    Processing helix  chain 'B' and resid 273 through 284
    Processing helix  chain 'B' and resid 287 through 298
      removed outlier: 3.640A  pdb=" N   ASP B 297 " --> pdb=" O   ALA B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 313
    Processing helix  chain 'B' and resid 315 through 328
    Processing helix  chain 'B' and resid 336 through 353
      removed outlier: 3.913A  pdb=" N   PHE B 340 " --> pdb=" O   GLN B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 370
      removed outlier: 3.610A  pdb=" N   MET B 370 " --> pdb=" O   GLN B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 374 through 388
    Processing helix  chain 'B' and resid 391 through 406
    Processing helix  chain 'B' and resid 502 through 517
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.568A  pdb=" N   PHE H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.798A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 85 through 89
    Processing helix  chain 'L' and resid 126 through 133
    Processing helix  chain 'L' and resid 188 through 194
      removed outlier: 3.722A  pdb=" N   HIS L 194 " --> pdb=" O   ASP L 190 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 62 through 65
      removed outlier: 3.531A  pdb=" N   LYS N  65 " --> pdb=" O   ASP N  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 62 through 65'
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 337 through 343
      removed outlier: 3.748A  pdb=" N   VAL R 341 " --> pdb=" O   PRO R 337 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 365 through 370
    Processing helix  chain 'R' and resid 383 through 387
      removed outlier: 3.798A  pdb=" N   LEU R 387 " --> pdb=" O   PRO R 384 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 405 through 410
      removed outlier: 4.935A  pdb=" N   ARG R 408 " --> pdb=" O   ASP R 405 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 416 through 422
    Processing helix  chain 'R' and resid 438 through 443
    Processing helix  chain 'R' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'B' and resid 37 through 39
      removed outlier: 5.958A  pdb=" N   ILE B  10 " --> pdb=" O   GLU B  39 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   VAL B   9 " --> pdb=" O   ILE B  60 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   PHE B  62 " --> pdb=" O   VAL B   9 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   TRP B  11 " --> pdb=" O   PHE B  62 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   ALA B 265 " --> pdb=" O   PRO B 108 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 37 through 39
      removed outlier: 5.958A  pdb=" N   ILE B  10 " --> pdb=" O   GLU B  39 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   VAL B   9 " --> pdb=" O   ILE B  60 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   PHE B  62 " --> pdb=" O   VAL B   9 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   TRP B  11 " --> pdb=" O   PHE B  62 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 99 through 100
    Processing sheet with id=AA4, first strand: chain 'B' and resid 225 through 228
    Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 173
      removed outlier: 4.055A  pdb=" N   LYS B 171 " --> pdb=" O   ASP B 178 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 250 through 251
    Processing sheet with id=AA7, first strand: chain 'B' and resid 522 through 526
    Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.770A  pdb=" N   GLY H  33 " --> pdb=" O   ARG H  99 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ALA H  40 " --> pdb=" O   GLY H  44 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 130 through 134
      removed outlier: 4.043A  pdb=" N   GLY H 149 " --> pdb=" O   LEU H 134 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 130 through 134
      removed outlier: 4.043A  pdb=" N   GLY H 149 " --> pdb=" O   LEU H 134 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 14
      removed outlier: 6.835A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 110 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   LYS L 112 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   VAL L  13 " --> pdb=" O   LYS L 112 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   LEU L  39 " --> pdb=" O   TYR L  55 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   TYR L  55 " --> pdb=" O   LEU L  39 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 14
      removed outlier: 6.835A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 110 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   LYS L 112 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   VAL L  13 " --> pdb=" O   LYS L 112 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 119 through 123
      removed outlier: 5.682A  pdb=" N   TYR L 178 " --> pdb=" O   ASN L 143 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 150 through 154
    Processing sheet with id=AB8, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB9, first strand: chain 'N' and resid 10 through 13
      removed outlier: 6.299A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 118 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   SER N 120 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL N  12 " --> pdb=" O   SER N 120 " (cutoff:3.500A)
      removed outlier: 4.853A  pdb=" N   LYS N  99 " --> pdb=" O   ARG N  33 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   ARG N  33 " --> pdb=" O   LYS N  99 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   MET N  34 " --> pdb=" O   ALA N  50 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   ALA N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'N' and resid 10 through 13
      removed outlier: 6.299A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 118 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   SER N 120 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL N  12 " --> pdb=" O   SER N 120 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'R' and resid 354 through 358
      removed outlier: 3.921A  pdb=" N   VAL R 395 " --> pdb=" O   ILE R 358 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'R' and resid 452 through 454
    Processing sheet with id=AC4, first strand: chain 'R' and resid 473 through 474

    423 hydrogen bonds defined for protein.
    1116 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: 1.51

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2864
        1.35 -     1.48: 2471
        1.48 -     1.61: 3844
        1.61 -     1.74: 0
        1.74 -     1.87: 47
  Bond restraints: 9226
  Sorted by residual:
  bond pdb=" CB  CYS R 379 "
       pdb=" SG  CYS R 379 "
    ideal  model  delta    sigma   weight residual
    1.808  1.875 -0.067 3.30e-02 9.18e+02 4.09e+00
  bond pdb=" CB  VAL N  48 "
       pdb=" CG2 VAL N  48 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.68e+00
  bond pdb=" CB  CYS R 432 "
       pdb=" SG  CYS R 432 "
    ideal  model  delta    sigma   weight residual
    1.808  1.768  0.040 3.30e-02 9.18e+02 1.48e+00
  bond pdb=" C1  GLC A   1 "
       pdb=" O1  GLC A   1 "
    ideal  model  delta    sigma   weight residual
    1.389  1.409 -0.020 2.00e-02 2.50e+03 9.63e-01
  bond pdb=" C   ILE B 133 "
       pdb=" N   PRO B 134 "
    ideal  model  delta    sigma   weight residual
    1.334  1.356 -0.022 2.34e-02 1.83e+03 9.00e-01
  ... (remaining 9221 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.65: 12431
        2.65 -     5.31: 91
        5.31 -     7.96: 3
        7.96 -    10.62: 0
       10.62 -    13.27: 2
  Bond angle restraints: 12527
  Sorted by residual:
  angle pdb=" N   CYS R 432 "
        pdb=" CA  CYS R 432 "
        pdb=" C   CYS R 432 "
      ideal   model   delta    sigma   weight residual
     107.88  119.63  -11.75 1.41e+00 5.03e-01 6.95e+01
  angle pdb=" CA  CYS R 432 "
        pdb=" CB  CYS R 432 "
        pdb=" SG  CYS R 432 "
      ideal   model   delta    sigma   weight residual
     114.40  127.67  -13.27 2.30e+00 1.89e-01 3.33e+01
  angle pdb=" C   GLY R 431 "
        pdb=" N   CYS R 432 "
        pdb=" CA  CYS R 432 "
      ideal   model   delta    sigma   weight residual
     122.45  118.44    4.01 1.78e+00 3.16e-01 5.07e+00
  angle pdb=" N   GLU B  23 "
        pdb=" CA  GLU B  23 "
        pdb=" CB  GLU B  23 "
      ideal   model   delta    sigma   weight residual
     110.16  113.37   -3.21 1.48e+00 4.57e-01 4.70e+00
  angle pdb=" C   GLU B 173 "
        pdb=" N   ASN B 174 "
        pdb=" CA  ASN B 174 "
      ideal   model   delta    sigma   weight residual
     121.54  125.58   -4.04 1.91e+00 2.74e-01 4.47e+00
  ... (remaining 12522 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4970
       17.94 -    35.87: 423
       35.87 -    53.81: 73
       53.81 -    71.75: 14
       71.75 -    89.68: 11
  Dihedral angle restraints: 5491
    sinusoidal: 2164
      harmonic: 3327
  Sorted by residual:
  dihedral pdb=" CA  GLU H 158 "
           pdb=" C   GLU H 158 "
           pdb=" N   PRO H 159 "
           pdb=" CA  PRO H 159 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.49   35.51     0      5.00e+00 4.00e-02 5.04e+01
  dihedral pdb=" CB  CYS R 379 "
           pdb=" SG  CYS R 379 "
           pdb=" SG  CYS R 432 "
           pdb=" CB  CYS R 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   34.17   58.83     1      1.00e+01 1.00e-02 4.63e+01
  dihedral pdb=" CB  CYS H 150 "
           pdb=" SG  CYS H 150 "
           pdb=" SG  CYS H 206 "
           pdb=" CB  CYS H 206 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  140.09  -47.09     1      1.00e+01 1.00e-02 3.06e+01
  ... (remaining 5488 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1180
       0.061 -    0.121: 177
       0.121 -    0.182: 8
       0.182 -    0.242: 0
       0.242 -    0.303: 2
  Chirality restraints: 1367
  Sorted by residual:
  chirality pdb=" C1  GLC A   2 "
            pdb=" O4  GLC A   1 "
            pdb=" C2  GLC A   2 "
            pdb=" O5  GLC A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.32    0.08 2.00e-02 2.50e+03 1.72e+01
  chirality pdb=" C1  GLC A   1 "
            pdb=" C2  GLC A   1 "
            pdb=" O1  GLC A   1 "
            pdb=" O5  GLC A   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.04   -2.34    0.30 2.00e-01 2.50e+01 2.30e+00
  chirality pdb=" CA  CYS R 432 "
            pdb=" N   CYS R 432 "
            pdb=" C   CYS R 432 "
            pdb=" CB  CYS R 432 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.79e+00
  ... (remaining 1364 not shown)

  Planarity restraints: 1604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 158 "    0.076 5.00e-02 4.00e+02   1.17e-01 2.19e+01
        pdb=" N   PRO H 159 "   -0.203 5.00e-02 4.00e+02
        pdb=" CA  PRO H 159 "    0.063 5.00e-02 4.00e+02
        pdb=" CD  PRO H 159 "    0.063 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER R 383 "   -0.053 5.00e-02 4.00e+02   8.02e-02 1.03e+01
        pdb=" N   PRO R 384 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO R 384 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO R 384 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 123 "    0.050 5.00e-02 4.00e+02   7.68e-02 9.43e+00
        pdb=" N   PRO B 124 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO B 124 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO B 124 "    0.042 5.00e-02 4.00e+02
  ... (remaining 1601 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 200
        2.69 -     3.24: 8625
        3.24 -     3.80: 14199
        3.80 -     4.35: 18927
        4.35 -     4.90: 31721
  Nonbonded interactions: 73672
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP R 442 "
            pdb=" OH  TYR R 451 "
     model   vdw
     2.138 3.040
  nonbonded pdb=" O   MET H 110 "
            pdb=" OH  TYR L  42 "
     model   vdw
     2.140 3.040
  nonbonded pdb=" ND2 ASN H 207 "
            pdb=" OD1 ASP H 218 "
     model   vdw
     2.145 3.120
  nonbonded pdb=" OE1 GLN L  27 "
            pdb=" OG1 THR N 118 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OD2 ASP R 398 "
            pdb=" OH  TYR R 423 "
     model   vdw
     2.208 3.040
  ... (remaining 73667 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.960
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.120
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
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      :  0.003   0.067   9234  Z= 0.140
  Angle     :  0.584  13.271  12544  Z= 0.305
  Chirality :  0.043   0.303   1367
  Planarity :  0.005   0.117   1604
  Dihedral  : 13.839  89.685   3344
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.21 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.25), residues: 1118
  helix:  0.60 (0.33), residues: 261
  sheet:  0.60 (0.27), residues: 346
  loop :  0.11 (0.29), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  38 
 TYR   0.015   0.001   TYR R 505 
 PHE   0.020   0.002   PHE B 259 
 TRP   0.016   0.001   TRP L  56 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 9226)
  covalent geometry    : angle       0.57510 (12527)
  SS BOND              : bond        0.00845 (    7)
  SS BOND              : angle       1.87767 (   14)
  hydrogen bonds       : bond        0.13486 (  401)
  hydrogen bonds       : angle       6.96838 ( 1116)
  link_ALPHA1-4        : bond        0.02745 (    1)
  link_ALPHA1-4        : angle       5.24159 (    3)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 142
  time to evaluate  : 0.329 
Fit side-chains
REVERT: B  327 LYS cc_start: 0.8157 (mttt) cc_final: 0.7643 (tptt)
REVERT: B  405 HIS cc_start: 0.8620 (t-90) cc_final: 0.8062 (t-170)
REVERT: B  485 LEU cc_start: 0.8913 (tp) cc_final: 0.8316 (tp)
REVERT: H    6 GLU cc_start: 0.7247 (mp0) cc_final: 0.6941 (mp0)
REVERT: H  153 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8255 (mmtp)
  outliers start: 2
  outliers final: 0
  residues processed: 143
  average time/residue: 0.0903
  time to fit residues: 18.4055
Evaluate side-chains
  111 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    0.8980
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN
B 204 HIS
** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 143 ASN
** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.191337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.161252 restraints weight = 11515.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.160008 restraints weight = 16390.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.162219 restraints weight = 12202.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.162231 restraints weight = 8589.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.162823 restraints weight = 8745.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.1067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080   9234  Z= 0.195
  Angle     :  0.600  14.636  12544  Z= 0.313
  Chirality :  0.043   0.162   1367
  Planarity :  0.005   0.102   1604
  Dihedral  :  4.572  33.707   1277
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  8.18 %
    Favored  : 90.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.25), residues: 1118
  helix:  1.10 (0.32), residues: 263
  sheet:  0.67 (0.27), residues: 340
  loop : -0.01 (0.28), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L 147 
 TYR   0.035   0.002   TYR R 505 
 PHE   0.024   0.002   PHE B 510 
 TRP   0.018   0.002   TRP N  47 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 9226)
  covalent geometry    : angle       0.59510 (12527)
  SS BOND              : bond        0.00895 (    7)
  SS BOND              : angle       2.25822 (   14)
  hydrogen bonds       : bond        0.03399 (  401)
  hydrogen bonds       : angle       5.49521 ( 1116)
  link_ALPHA1-4        : bond        0.00483 (    1)
  link_ALPHA1-4        : angle       1.64164 (    3)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 0.377 
Fit side-chains
REVERT: B  318 ILE cc_start: 0.8668 (mm) cc_final: 0.8342 (mp)
REVERT: B  405 HIS cc_start: 0.8662 (t-90) cc_final: 0.8128 (t-170)
REVERT: B  532 PHE cc_start: 0.7544 (m-80) cc_final: 0.7167 (m-80)
REVERT: H    6 GLU cc_start: 0.7238 (mp0) cc_final: 0.7003 (mp0)
REVERT: H  219 LYS cc_start: 0.7506 (tppt) cc_final: 0.7292 (tppt)
REVERT: R  357 ARG cc_start: 0.6715 (ttp-170) cc_final: 0.6495 (ttp-170)
  outliers start: 12
  outliers final: 10
  residues processed: 140
  average time/residue: 0.0886
  time to fit residues: 17.6978
Evaluate side-chains
  128 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain H residue   89 GLU
Chi-restraints excluded: chain H residue  110 MET
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain R residue  392 PHE
Chi-restraints excluded: chain R residue  401 VAL
Chi-restraints excluded: chain R residue  432 CYS
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 35 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 61 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 11 optimal weight:    8.9990
   chunk 82 optimal weight:    9.9990
   chunk 111 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
B 204 HIS
** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 174 HIS
L  32 ASN
** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.193112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.159688 restraints weight = 11820.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.156970 restraints weight = 13030.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.153152 restraints weight = 10512.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.153821 restraints weight = 9340.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.154537 restraints weight = 7473.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.1349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   9234  Z= 0.177
  Angle     :  0.570  13.568  12544  Z= 0.298
  Chirality :  0.043   0.224   1367
  Planarity :  0.005   0.092   1604
  Dihedral  :  4.530  32.294   1277
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 12.11 %
    Favored  : 86.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.25), residues: 1118
  helix:  1.16 (0.32), residues: 265
  sheet:  0.56 (0.26), residues: 354
  loop : -0.01 (0.28), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 147 
 TYR   0.026   0.001   TYR R 505 
 PHE   0.017   0.002   PHE L 144 
 TRP   0.020   0.002   TRP N  47 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 9226)
  covalent geometry    : angle       0.56532 (12527)
  SS BOND              : bond        0.00820 (    7)
  SS BOND              : angle       2.19636 (   14)
  hydrogen bonds       : bond        0.03130 (  401)
  hydrogen bonds       : angle       5.27251 ( 1116)
  link_ALPHA1-4        : bond        0.00323 (    1)
  link_ALPHA1-4        : angle       1.59534 (    3)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 135
  time to evaluate  : 0.326 
Fit side-chains
REVERT: B  405 HIS cc_start: 0.8693 (t-90) cc_final: 0.8232 (t-170)
REVERT: H  219 LYS cc_start: 0.7611 (tppt) cc_final: 0.7311 (tppt)
REVERT: R  357 ARG cc_start: 0.6950 (ttp-170) cc_final: 0.6592 (ttp-170)
  outliers start: 16
  outliers final: 14
  residues processed: 142
  average time/residue: 0.0818
  time to fit residues: 17.0784
Evaluate side-chains
  136 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   89 GLU
Chi-restraints excluded: chain H residue  110 MET
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   66 ASP
Chi-restraints excluded: chain L residue   95 HIS
Chi-restraints excluded: chain R residue  392 PHE
Chi-restraints excluded: chain R residue  401 VAL
Chi-restraints excluded: chain R residue  432 CYS
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 87 optimal weight:    0.6980
   chunk 88 optimal weight:    0.1980
   chunk 26 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   chunk 65 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 19 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 104 optimal weight:    7.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
B 204 HIS
** R 422 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 = 0.4322 r_free = 0.4322 target = 0.195951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.170329 restraints weight = 11930.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.169979 restraints weight = 17084.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.171937 restraints weight = 12957.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.171922 restraints weight = 9152.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.172619 restraints weight = 9886.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.4077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7326
moved from start:          0.1542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.094   9234  Z= 0.118
  Angle     :  0.537  12.540  12544  Z= 0.278
  Chirality :  0.041   0.131   1367
  Planarity :  0.004   0.081   1604
  Dihedral  :  4.352  30.448   1277
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 14.29 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.25), residues: 1118
  helix:  1.45 (0.33), residues: 259
  sheet:  0.57 (0.27), residues: 354
  loop :  0.07 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 147 
 TYR   0.019   0.001   TYR R 505 
 PHE   0.022   0.001   PHE L 144 
 TRP   0.018   0.001   TRP N  47 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9226)
  covalent geometry    : angle       0.52940 (12527)
  SS BOND              : bond        0.01070 (    7)
  SS BOND              : angle       2.72949 (   14)
  hydrogen bonds       : bond        0.02803 (  401)
  hydrogen bonds       : angle       5.03638 ( 1116)
  link_ALPHA1-4        : bond        0.00023 (    1)
  link_ALPHA1-4        : angle       1.39805 (    3)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 0.334 
Fit side-chains
REVERT: B  405 HIS cc_start: 0.8648 (t-90) cc_final: 0.8217 (t-170)
REVERT: B  485 LEU cc_start: 0.8737 (tp) cc_final: 0.8361 (tp)
REVERT: R  357 ARG cc_start: 0.6917 (ttp-170) cc_final: 0.6612 (ttp-170)
  outliers start: 12
  outliers final: 10
  residues processed: 134
  average time/residue: 0.0790
  time to fit residues: 15.6615
Evaluate side-chains
  129 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  225 MET
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   95 HIS
Chi-restraints excluded: chain R residue  432 CYS
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 30 optimal weight:    0.4980
   chunk 76 optimal weight:    9.9990
   chunk 79 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9980
   chunk 39 optimal weight:    8.9990
   chunk 99 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9980
   chunk 14 optimal weight:    7.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
** R 422 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 = 0.4302 r_free = 0.4302 target = 0.193673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.167143 restraints weight = 11915.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.163680 restraints weight = 14394.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.161643 restraints weight = 12651.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.161414 restraints weight = 11716.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.160852 restraints weight = 10494.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.1713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086   9234  Z= 0.154
  Angle     :  0.562  13.375  12544  Z= 0.290
  Chirality :  0.041   0.145   1367
  Planarity :  0.004   0.062   1604
  Dihedral  :  4.384  30.992   1277
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.73 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.25), residues: 1118
  helix:  1.65 (0.33), residues: 252
  sheet:  0.58 (0.27), residues: 354
  loop :  0.02 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  38 
 TYR   0.017   0.001   TYR R 505 
 PHE   0.022   0.001   PHE B 510 
 TRP   0.017   0.001   TRP N  47 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 9226)
  covalent geometry    : angle       0.55580 (12527)
  SS BOND              : bond        0.00898 (    7)
  SS BOND              : angle       2.52482 (   14)
  hydrogen bonds       : bond        0.02895 (  401)
  hydrogen bonds       : angle       4.99304 ( 1116)
  link_ALPHA1-4        : bond        0.00095 (    1)
  link_ALPHA1-4        : angle       1.38942 (    3)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: B  405 HIS cc_start: 0.8693 (t-90) cc_final: 0.8289 (t-170)
REVERT: L   69 THR cc_start: 0.8069 (t) cc_final: 0.7863 (p)
REVERT: R  351 TYR cc_start: 0.8053 (p90) cc_final: 0.7790 (p90)
REVERT: R  357 ARG cc_start: 0.7049 (ttp-170) cc_final: 0.6749 (ttp-170)
  outliers start: 20
  outliers final: 18
  residues processed: 137
  average time/residue: 0.0789
  time to fit residues: 15.6173
Evaluate side-chains
  139 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  225 MET
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   56 THR
Chi-restraints excluded: chain H residue  110 MET
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   66 ASP
Chi-restraints excluded: chain L residue   95 HIS
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain R residue  401 VAL
Chi-restraints excluded: chain R residue  432 CYS
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 106 optimal weight:    0.8980
   chunk 84 optimal weight:    0.7980
   chunk 104 optimal weight:    4.9990
   chunk 11 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 32 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 99 optimal weight:    5.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
B 125 ASN
B 324 ASN
** L  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.171881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.139019 restraints weight = 11328.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.134121 restraints weight = 13688.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.132573 restraints weight = 13160.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.133167 restraints weight = 10870.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.133020 restraints weight = 9222.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.083   9234  Z= 0.236
  Angle     :  0.621  13.177  12544  Z= 0.323
  Chirality :  0.044   0.144   1367
  Planarity :  0.004   0.061   1604
  Dihedral  :  4.729  30.540   1277
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 15.84 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.25), residues: 1118
  helix:  1.45 (0.33), residues: 253
  sheet:  0.47 (0.27), residues: 351
  loop : -0.16 (0.28), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 457 
 TYR   0.022   0.002   TYR L  97 
 PHE   0.023   0.002   PHE B 532 
 TRP   0.019   0.002   TRP N  47 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00560 ( 9226)
  covalent geometry    : angle       0.61516 (12527)
  SS BOND              : bond        0.00897 (    7)
  SS BOND              : angle       2.47739 (   14)
  hydrogen bonds       : bond        0.03263 (  401)
  hydrogen bonds       : angle       5.23064 ( 1116)
  link_ALPHA1-4        : bond        0.00546 (    1)
  link_ALPHA1-4        : angle       1.48321 (    3)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 130
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: B   90 LEU cc_start: 0.7758 (mt) cc_final: 0.7322 (mt)
REVERT: L   69 THR cc_start: 0.8133 (t) cc_final: 0.7905 (p)
REVERT: R  351 TYR cc_start: 0.8094 (p90) cc_final: 0.7837 (p90)
REVERT: R  357 ARG cc_start: 0.7007 (ttp-170) cc_final: 0.6701 (ttp-170)
  outliers start: 30
  outliers final: 20
  residues processed: 148
  average time/residue: 0.0852
  time to fit residues: 17.8644
Evaluate side-chains
  140 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  225 MET
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   56 THR
Chi-restraints excluded: chain H residue   89 GLU
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  176 PHE
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   95 HIS
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain R residue  401 VAL
Chi-restraints excluded: chain R residue  432 CYS
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 86 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 109 optimal weight:    0.6980
   chunk 101 optimal weight:    0.9990
   chunk 110 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 81 optimal weight:    8.9990
   chunk 70 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 99 optimal weight:    5.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
B 125 ASN
L 171 GLN
** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.176289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.142536 restraints weight = 11289.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.138398 restraints weight = 13724.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.134855 restraints weight = 12209.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.135312 restraints weight = 11700.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.136505 restraints weight = 8768.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.103   9234  Z= 0.128
  Angle     :  0.564  13.166  12544  Z= 0.292
  Chirality :  0.041   0.158   1367
  Planarity :  0.004   0.092   1604
  Dihedral  :  4.503  31.889   1277
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 16.77 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.25), residues: 1118
  helix:  1.41 (0.33), residues: 261
  sheet:  0.50 (0.27), residues: 348
  loop : -0.06 (0.29), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N  38 
 TYR   0.016   0.001   TYR B 100 
 PHE   0.019   0.001   PHE L 144 
 TRP   0.020   0.001   TRP N  47 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 9226)
  covalent geometry    : angle       0.55765 (12527)
  SS BOND              : bond        0.00857 (    7)
  SS BOND              : angle       2.58068 (   14)
  hydrogen bonds       : bond        0.02827 (  401)
  hydrogen bonds       : angle       5.04170 ( 1116)
  link_ALPHA1-4        : bond        0.00115 (    1)
  link_ALPHA1-4        : angle       1.33508 (    3)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
REVERT: B   90 LEU cc_start: 0.7788 (mt) cc_final: 0.7337 (mt)
REVERT: L   69 THR cc_start: 0.8056 (t) cc_final: 0.7854 (p)
REVERT: R  351 TYR cc_start: 0.8070 (p90) cc_final: 0.7843 (p90)
REVERT: R  357 ARG cc_start: 0.7040 (ttp-170) cc_final: 0.6737 (ttp-170)
  outliers start: 22
  outliers final: 16
  residues processed: 142
  average time/residue: 0.0777
  time to fit residues: 16.0908
Evaluate side-chains
  140 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  225 MET
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   56 THR
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   94 CYS
Chi-restraints excluded: chain L residue   95 HIS
Chi-restraints excluded: chain R residue  432 CYS
Chi-restraints excluded: chain R residue  461 LEU
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 88 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 63 optimal weight:    0.5980
   chunk 40 optimal weight:    6.9990
   chunk 96 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 43 optimal weight:    7.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.176983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.142167 restraints weight = 11296.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.141256 restraints weight = 13690.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.137703 restraints weight = 11240.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.137921 restraints weight = 12187.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.138779 restraints weight = 9133.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.093   9234  Z= 0.125
  Angle     :  0.566  13.675  12544  Z= 0.291
  Chirality :  0.042   0.150   1367
  Planarity :  0.004   0.090   1604
  Dihedral  :  4.402  31.246   1277
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 16.98 %
    Favored  : 80.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.25), residues: 1118
  helix:  1.47 (0.33), residues: 259
  sheet:  0.52 (0.27), residues: 354
  loop : -0.06 (0.29), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 457 
 TYR   0.021   0.001   TYR H  80 
 PHE   0.018   0.001   PHE L 144 
 TRP   0.017   0.001   TRP N  47 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9226)
  covalent geometry    : angle       0.55891 (12527)
  SS BOND              : bond        0.00967 (    7)
  SS BOND              : angle       2.68632 (   14)
  hydrogen bonds       : bond        0.02819 (  401)
  hydrogen bonds       : angle       4.93414 ( 1116)
  link_ALPHA1-4        : bond        0.00019 (    1)
  link_ALPHA1-4        : angle       1.27901 (    3)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 0.321 
Fit side-chains
REVERT: B  291 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7189 (mm)
REVERT: H  219 LYS cc_start: 0.7777 (tppt) cc_final: 0.7459 (tppt)
REVERT: L   69 THR cc_start: 0.8036 (t) cc_final: 0.7805 (p)
REVERT: R  351 TYR cc_start: 0.8103 (p90) cc_final: 0.7828 (p90)
REVERT: R  357 ARG cc_start: 0.7004 (ttp-170) cc_final: 0.6759 (ttp-170)
  outliers start: 22
  outliers final: 16
  residues processed: 145
  average time/residue: 0.0769
  time to fit residues: 16.3108
Evaluate side-chains
  140 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  225 MET
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   56 THR
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   94 CYS
Chi-restraints excluded: chain L residue   95 HIS
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain R residue  432 CYS
Chi-restraints excluded: chain R residue  461 LEU
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 50 optimal weight:    7.9990
   chunk 39 optimal weight:   20.0000
   chunk 110 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 96 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9980
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  95 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.174329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.144824 restraints weight = 11298.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.141200 restraints weight = 14785.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.137878 restraints weight = 14082.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.138329 restraints weight = 13502.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.138316 restraints weight = 10102.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.095   9234  Z= 0.178
  Angle     :  0.608  13.921  12544  Z= 0.311
  Chirality :  0.043   0.159   1367
  Planarity :  0.005   0.090   1604
  Dihedral  :  4.590  31.316   1277
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.29 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.25), residues: 1118
  helix:  1.44 (0.33), residues: 259
  sheet:  0.52 (0.27), residues: 345
  loop : -0.24 (0.28), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 457 
 TYR   0.025   0.002   TYR H  80 
 PHE   0.020   0.002   PHE B 532 
 TRP   0.017   0.001   TRP N  47 
 HIS   0.002   0.001   HIS L  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 9226)
  covalent geometry    : angle       0.60104 (12527)
  SS BOND              : bond        0.01019 (    7)
  SS BOND              : angle       2.79086 (   14)
  hydrogen bonds       : bond        0.02966 (  401)
  hydrogen bonds       : angle       5.00425 ( 1116)
  link_ALPHA1-4        : bond        0.00200 (    1)
  link_ALPHA1-4        : angle       1.32077 (    3)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: B  291 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7222 (mm)
REVERT: R  351 TYR cc_start: 0.8120 (p90) cc_final: 0.7830 (p90)
REVERT: R  357 ARG cc_start: 0.7016 (ttp-170) cc_final: 0.6766 (ttp-170)
  outliers start: 21
  outliers final: 18
  residues processed: 138
  average time/residue: 0.0791
  time to fit residues: 16.0837
Evaluate side-chains
  135 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue  225 MET
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   56 THR
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  151 LEU
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   94 CYS
Chi-restraints excluded: chain L residue   95 HIS
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain R residue  432 CYS
Chi-restraints excluded: chain R residue  461 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 67 optimal weight:    0.9980
   chunk 42 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 107 optimal weight:    0.5980
   chunk 40 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 82 optimal weight:   10.0000
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 366 GLN
** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.172230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.139203 restraints weight = 11322.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.135618 restraints weight = 14544.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.132314 restraints weight = 12409.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.133107 restraints weight = 11019.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.133334 restraints weight = 8533.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.098   9234  Z= 0.233
  Angle     :  0.648  14.093  12544  Z= 0.332
  Chirality :  0.044   0.175   1367
  Planarity :  0.005   0.094   1604
  Dihedral  :  4.796  34.462   1277
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.49 %
    Favored  : 80.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.25), residues: 1118
  helix:  1.38 (0.33), residues: 258
  sheet:  0.38 (0.27), residues: 347
  loop : -0.34 (0.28), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  19 
 TYR   0.027   0.002   TYR L  97 
 PHE   0.022   0.002   PHE B 532 
 TRP   0.018   0.002   TRP N  47 
 HIS   0.009   0.001   HIS L  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 ( 9226)
  covalent geometry    : angle       0.64093 (12527)
  SS BOND              : bond        0.01049 (    7)
  SS BOND              : angle       2.90627 (   14)
  hydrogen bonds       : bond        0.03148 (  401)
  hydrogen bonds       : angle       5.16519 ( 1116)
  link_ALPHA1-4        : bond        0.00318 (    1)
  link_ALPHA1-4        : angle       1.42543 (    3)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.323 
Fit side-chains
REVERT: B  291 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7262 (mm)
REVERT: H  219 LYS cc_start: 0.7787 (tppt) cc_final: 0.7509 (tppt)
REVERT: R  351 TYR cc_start: 0.8155 (p90) cc_final: 0.7885 (p90)
REVERT: R  357 ARG cc_start: 0.7023 (ttp-170) cc_final: 0.6718 (ttp-170)
  outliers start: 21
  outliers final: 19
  residues processed: 131
  average time/residue: 0.0753
  time to fit residues: 14.4112
Evaluate side-chains
  136 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue  225 MET
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   56 THR
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  151 LEU
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   94 CYS
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain R residue  401 VAL
Chi-restraints excluded: chain R residue  432 CYS
Chi-restraints excluded: chain R residue  459 SER
Chi-restraints excluded: chain R residue  461 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    8.9990
   chunk 57 optimal weight:    0.9980
   chunk 80 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 76 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 30 optimal weight:    0.2980
   chunk 72 optimal weight:    1.9990
   chunk 105 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.176589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 89)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.143962 restraints weight = 11046.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.138022 restraints weight = 13718.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.134657 restraints weight = 13347.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.135675 restraints weight = 11342.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.135865 restraints weight = 9176.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.093   9234  Z= 0.124
  Angle     :  0.584  13.748  12544  Z= 0.298
  Chirality :  0.042   0.162   1367
  Planarity :  0.004   0.092   1604
  Dihedral  :  4.523  31.654   1277
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 17.70 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.25), residues: 1118
  helix:  1.49 (0.33), residues: 259
  sheet:  0.40 (0.27), residues: 346
  loop : -0.22 (0.28), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 457 
 TYR   0.016   0.001   TYR B 100 
 PHE   0.018   0.001   PHE L 144 
 TRP   0.020   0.001   TRP N  47 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 9226)
  covalent geometry    : angle       0.57747 (12527)
  SS BOND              : bond        0.00990 (    7)
  SS BOND              : angle       2.68672 (   14)
  hydrogen bonds       : bond        0.02769 (  401)
  hydrogen bonds       : angle       4.97069 ( 1116)
  link_ALPHA1-4        : bond        0.00001 (    1)
  link_ALPHA1-4        : angle       1.24789 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1481.65 seconds
wall clock time: 26 minutes 19.32 seconds (1579.32 seconds total)